From bb2d82da7f4edde53b83f5ebeea4a4d97a91e182 Mon Sep 17 00:00:00 2001
From: Steph Prince <40640337+stephprince@users.noreply.github.com>
Date: Sat, 21 Dec 2024 15:03:35 -0800
Subject: [PATCH] remove warnings on construct for deprecations

---
 src/pynwb/core.py                          |  6 ++-
 src/pynwb/file.py                          | 13 ++++++-
 tests/integration/hdf5/test_ecephys.py     | 37 +++++++------------
 tests/integration/hdf5/test_icephys.py     | 40 +++++++-------------
 tests/unit/test_base.py                    | 12 ++++--
 tests/unit/test_ecephys.py                 | 12 +++---
 tests/unit/test_file.py                    | 43 ++++++----------------
 tests/unit/test_icephys.py                 | 34 ++---------------
 tests/unit/test_icephys_metadata_tables.py | 38 ++++++-------------
 tests/unit/test_image.py                   | 16 ++++----
 tests/unit/test_ophys.py                   | 12 +++---
 tests/unit/test_scratch.py                 | 16 ++++----
 12 files changed, 108 insertions(+), 171 deletions(-)

diff --git a/src/pynwb/core.py b/src/pynwb/core.py
index deb3a8c22..73327f8f8 100644
--- a/src/pynwb/core.py
+++ b/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
 
 
diff --git a/src/pynwb/file.py b/src/pynwb/file.py
index c5e6db889..b670b460b 100644
--- a/src/pynwb/file.py
+++ b/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')
diff --git a/tests/integration/hdf5/test_ecephys.py b/tests/integration/hdf5/test_ecephys.py
index 8f2bcdfb4..9bfdf3086 100644
--- a/tests/integration/hdf5/test_ecephys.py
+++ b/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):
diff --git a/tests/integration/hdf5/test_icephys.py b/tests/integration/hdf5/test_icephys.py
index 17281b7ec..c40a51b53 100644
--- a/tests/integration/hdf5/test_icephys.py
+++ b/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 """
diff --git a/tests/unit/test_base.py b/tests/unit/test_base.py
index 28c4e91d4..a1afe1d15 100644
--- a/tests/unit/test_base.py
+++ b/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)
 
@@ -68,8 +70,9 @@ 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)
@@ -77,8 +80,9 @@ def test_deprecated_get_data_interface(self):
     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)
diff --git a/tests/unit/test_ecephys.py b/tests/unit/test_ecephys.py
index 147268931..f54a56996 100644
--- a/tests/unit/test_ecephys.py
+++ b/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')
diff --git a/tests/unit/test_file.py b/tests/unit/test_file.py
index e2feb1930..9e4bf1a28 100644
--- a/tests/unit/test_file.py
+++ b/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):
diff --git a/tests/unit/test_icephys.py b/tests/unit/test_icephys.py
index ec0d68e77..5b77a1e94 100644
--- a/tests/unit/test_icephys.py
+++ b/tests/unit/test_icephys.py
@@ -47,9 +47,9 @@ def test_sweep_table_deprecation_warn(self):
             SweepTable()
 
         # create object in construct mode, modeling the behavior of the ObjectMapper on read
+        # should not raise error or warning
         sweepT = SweepTable.__new__(SweepTable, in_construct_mode=True)
-        with self.assertWarnsWith(warn_type=UserWarning, exc_msg=msg):
-            sweepT.__init__()
+        sweepT.__init__()
         
         kwargs = dict(session_description='NWBFile icephys test',
                 identifier='NWB123',  # required
@@ -61,25 +61,9 @@ def test_sweep_table_deprecation_warn(self):
             NWBFile(**kwargs)
 
         # create object in construct mode, modeling the behavior of the ObjectMapper on read
+        # should not warn or error
         nwbfile = NWBFile.__new__(NWBFile, in_construct_mode=True)
-        
-        with self.assertWarnsWith(warn_type=UserWarning, exc_msg=msg):
-            nwbfile.__init__(**kwargs)
-
-    def test_ic_electrodes_parameter_deprecation(self):
-        # Make sure we warn when using the ic_electrodes parameter on NWBFile
-        msg = "Use of the ic_electrodes parameter is deprecated. Use the icephys_electrodes parameter instead"
-        kwargs = dict(session_description='NWBFile icephys test',
-                identifier='NWB123',  # required
-                session_start_time=datetime(2017, 4, 3, 11, tzinfo=tzlocal()),
-                ic_electrodes=[self.icephys_electrode, ])
-        with self.assertRaisesWith(ValueError, msg):
-            NWBFile(**kwargs)
-
-        # 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)
+        nwbfile.__init__(**kwargs)
 
     def test_icephys_electrodes_parameter(self):
         nwbfile = NWBFile(
@@ -95,16 +79,6 @@ def test_ic_electrodes_attribute_deprecation(self):
             identifier='NWB123',  # required
             session_start_time=datetime(2017, 4, 3, 11, tzinfo=tzlocal()),
             icephys_electrodes=[self.icephys_electrode, ])
-        
-        # make sure NWBFile.ic_electrodes property warns or errors
-        msg = "NWBFile.ic_electrodes is deprecated. Use NWBFile.icephys_electrodes instead."
-        with self.assertRaisesWith(ValueError, msg):
-            nwbfile.ic_electrodes
-
-        nwbfile._in_construct_mode = True
-        with self.assertWarnsWith(warn_type=UserWarning, exc_msg=msg):
-            nwbfile.ic_electrodes
-        nwbfile._in_construct_mode = False
 
         # make sure NWBFile.get_ic_electrode warns
         msg = "'NWBFile' object has no attribute 'get_ic_electrode'"
diff --git a/tests/unit/test_icephys_metadata_tables.py b/tests/unit/test_icephys_metadata_tables.py
index ba8d866fb..e73a95c29 100644
--- a/tests/unit/test_icephys_metadata_tables.py
+++ b/tests/unit/test_icephys_metadata_tables.py
@@ -1117,9 +1117,9 @@ def test_deprecate_simultaneous_recordings_on_add_stimulus(self):
         with self.assertRaisesWith(ValueError, msg):
             nwbfile.add_stimulus(stimulus, use_sweep_table=True)
         
+        # shoudl not error when in construct mode
         nwbfile._in_construct_mode = True
-        with self.assertWarnsWith(warn_type=UserWarning, exc_msg=msg):
-            nwbfile.add_stimulus(stimulus2, use_sweep_table=True)
+        nwbfile.add_stimulus(stimulus2, use_sweep_table=True)
         
         # make sure we don't trigger the same deprecation warning twice
         nwbfile.add_acquisition(response, use_sweep_table=True)
@@ -1153,15 +1153,6 @@ def test_deprecate_sweeptable_on_add_stimulus_template(self):
             gain=0.02,
             sweep_number=np.uint64(15)
         )
-        local_stimulus3 = VoltageClampStimulusSeries(
-            name="ccss3",
-            data=[1, 2, 3, 4, 5],
-            starting_time=123.6,
-            rate=10e3,
-            electrode=local_electrode,
-            gain=0.02,
-            sweep_number=np.uint64(15)
-        )
 
         msg = ("SweepTable is deprecated. Use the IntracellularRecordingsTable instead. "
                "See also the NWBFile.add_intracellular_recordings function.")
@@ -1170,12 +1161,9 @@ def test_deprecate_sweeptable_on_add_stimulus_template(self):
             # NOTE - the sweep table creation will error but the stimulus template will still be added
 
         # create object in construct mode, modeling the behavior of the ObjectMapper on read
+        # should not trigger any warnings or errors
         nwbfile._in_construct_mode = True
-        with self.assertWarnsWith(warn_type=UserWarning, exc_msg=msg):
-            nwbfile.add_stimulus_template(local_stimulus2, use_sweep_table=True)
-
-        # make sure we don't trigger the same warning twice (should only be triggered on table creation)
-        nwbfile.add_stimulus_template(local_stimulus3, use_sweep_table=True)
+        nwbfile.add_stimulus_template(local_stimulus2, use_sweep_table=True)
         nwbfile._in_construct_mode = False
 
     def test_deprecate_sweepstable_on_add_acquistion(self):
@@ -1209,9 +1197,9 @@ def test_deprecate_sweepstable_on_add_acquistion(self):
             nwbfile.add_acquisition(response, use_sweep_table=True)
             # NOTE - the sweep table creation will error but the acquisition will still be added
         
+        # should not trigger error or warning in construct mode
         nwbfile._in_construct_mode = True
-        with self.assertWarnsWith(warn_type=UserWarning, exc_msg=msg):
-            nwbfile.add_acquisition(response2, use_sweep_table=True)
+        nwbfile.add_acquisition(response2, use_sweep_table=True)
         
         # make sure we don't trigger the same deprecation warning twice
         nwbfile.add_stimulus(stimulus, use_sweep_table=True)
@@ -1223,12 +1211,8 @@ def test_deprecate_sweepstable_on_init(self):
         Test that warnings are raised if the user tries to use a sweeps table
         """
         from pynwb.icephys import SweepTable
-        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):
-            sweepT = SweepTable.__new__(SweepTable, in_construct_mode=True)
-            sweepT.__init__()
+        sweepT = SweepTable.__new__(SweepTable, in_construct_mode=True)
+        sweepT.__init__()
 
         kwargs = dict(session_description='my first synthetic recording',
                 identifier='EXAMPLE_ID',
@@ -1236,13 +1220,15 @@ def test_deprecate_sweepstable_on_init(self):
                 sweep_table=sweepT)
         
         # check we raise an error when using the sweeptable argument on init
+        msg = ("SweepTable is deprecated. Use the IntracellularRecordingsTable instead. "
+            "See also the NWBFile.add_intracellular_recordings function.")
         with self.assertRaisesWith(ValueError, msg):
             nwbfile = NWBFile(**kwargs)
 
         # create object in construct mode, modeling the behavior of the ObjectMapper on read
+        # should not trigger warning or error
         nwbfile = NWBFile.__new__(NWBFile, in_construct_mode=True)
-        with self.assertWarnsWith(warn_type=UserWarning, exc_msg=msg):
-            nwbfile.__init__(**kwargs)
+        nwbfile.__init__(**kwargs)
 
         # make sure we don't trigger the same deprecation warning twice
         device = self.__add_device(nwbfile)
diff --git a/tests/unit/test_image.py b/tests/unit/test_image.py
index 70bd01043..a2e24a209 100644
--- a/tests/unit/test_image.py
+++ b/tests/unit/test_image.py
@@ -243,7 +243,8 @@ def test_external_file_default_format(self):
         """Test that format is set to 'external' if not provided, when external_file is provided."""
         msg = (
             "ImageSeries 'test_iS': The value for 'format' has been changed to 'external'. "
-            "Setting a default value for 'format' is deprecated."
+            "If an external file is detected, setting a value for "
+            "'format' other than 'external' is deprecated."
         )
         kwargs = dict(name="test_iS",
                 external_file=["external_file", "external_file2"],
@@ -326,9 +327,10 @@ def test_bits_per_pixel_deprecation(self):
         with self.assertRaisesWith(ValueError, msg):
             ImageSeries(**kwargs)
 
+        # create object in construct mode, modeling the behavior of the ObjectMapper on read
+        # no warning or error should be raised
         iS = ImageSeries.__new__(ImageSeries, in_construct_mode=True)
-        with self.assertWarnsWith(UserWarning, msg):
-            iS.__init__(**kwargs)
+        iS.__init__(**kwargs)
 
 
 class IndexSeriesConstructor(TestCase):
@@ -369,9 +371,9 @@ def test_init_bad_unit(self):
             IndexSeries(**kwargs)
 
         # create object in construct mode, modeling the behavior of the ObjectMapper on read
+        # no warning or error should be raised
         iS = IndexSeries.__new__(IndexSeries, in_construct_mode=True)
-        with self.assertWarnsWith(warn_type=UserWarning, exc_msg=msg):
-            iS.__init__(**kwargs)
+        iS.__init__(**kwargs)
 
         self.assertEqual(iS.unit, 'N/A')
 
@@ -395,9 +397,9 @@ def test_init_indexed_ts(self):
             IndexSeries(**kwargs)
 
         # create object in construct mode, modeling the behavior of the ObjectMapper on read
+        # no warning or error should be raised
         iS = IndexSeries.__new__(IndexSeries, in_construct_mode=True)
-        with self.assertWarnsWith(warn_type=UserWarning, exc_msg=msg):
-            iS.__init__(**kwargs)
+        iS.__init__(**kwargs)
 
         self.assertIs(iS.indexed_timeseries, ts)
 
diff --git a/tests/unit/test_ophys.py b/tests/unit/test_ophys.py
index 9d4bf5ee6..d484d9e01 100644
--- a/tests/unit/test_ophys.py
+++ b/tests/unit/test_ophys.py
@@ -147,9 +147,9 @@ def test_manifold_deprecated(self):
             ImagingPlane(**kwargs)
 
         # create object in construct mode, modeling the behavior of the ObjectMapper on read
+        # no warning or error should be raised
         obj = ImagingPlane.__new__(ImagingPlane, in_construct_mode=True)
-        with self.assertWarnsWith(warn_type=UserWarning, exc_msg=msg):
-            obj.__init__(**kwargs)
+        obj.__init__(**kwargs)
 
     def test_conversion_deprecated(self):
         oc, device = self.set_up_dependencies()
@@ -169,9 +169,9 @@ def test_conversion_deprecated(self):
             ImagingPlane(**kwargs)
 
         # create object in construct mode, modeling the behavior of the ObjectMapper on read
+        # no warning or error should be raised
         obj = ImagingPlane.__new__(ImagingPlane, in_construct_mode=True)
-        with self.assertWarnsWith(warn_type=UserWarning, exc_msg=msg):
-            obj.__init__(**kwargs)
+        obj.__init__(**kwargs)
 
     def test_unit_deprecated(self):
         oc, device = self.set_up_dependencies()
@@ -192,9 +192,9 @@ def test_unit_deprecated(self):
             ImagingPlane(**kwargs)
 
         # create object in construct mode, modeling the behavior of the ObjectMapper on read
+        # no warning or error should be raised
         obj = ImagingPlane.__new__(ImagingPlane, in_construct_mode=True)
-        with self.assertWarnsWith(warn_type=UserWarning, exc_msg=msg):
-            obj.__init__(**kwargs)
+        obj.__init__(**kwargs)
 
 
 class OnePhotonSeriesConstructor(TestCase):
diff --git a/tests/unit/test_scratch.py b/tests/unit/test_scratch.py
index 8de6be7df..e17c0b518 100644
--- a/tests/unit/test_scratch.py
+++ b/tests/unit/test_scratch.py
@@ -29,18 +29,20 @@ def test_constructor_list(self):
         self.assertEqual(sd.description, 'test scratch')
 
     def test_scratch_notes_deprecation(self):
-        msg = "The `notes` argument of ScratchData.__init__ has been deprecated. Use description instead."
+        msg = ("The `notes` argument of ScratchData.__init__ has been deprecated and will "
+               "be removed in PyNWB 4.0. Use description instead.")
         with self.assertRaisesWith(ValueError, msg):
             ScratchData(name='test', data=[1, 2, 3, 4, 5], notes='test notes')
 
         # create object in construct mode, modeling the behavior of the ObjectMapper on read 
+        # should not raise error or warning
         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')
+        data.__init__(name='test', data=[1, 2, 3, 4, 5], notes='test notes')
         self.assertEqual(data.description, 'test notes')
 
         # test notes property
-        msg = "Use of ScratchData.notes has been deprecated. Use ScratchData.description instead."
+        msg = ("Use of ScratchData.notes has been deprecated and will be removed in PyNWB 4.0. "
+               "Use ScratchData.description instead.")
         with self.assertWarnsWith(DeprecationWarning, msg):
             data.notes
 
@@ -146,15 +148,15 @@ def test_add_scratch_dynamictable(self):
         self.assertIs(self.nwbfile.scratch['test'], data)
     
     def test_add_scratch_notes_deprecation(self):
-        msg =  ("Use of the `notes` or `table_description` argument is deprecated. "
+        msg =  ("Use of the `notes` or `table_description` argument is deprecated and will be removed in PyNWB 4.0. "
                 "Use the `description` argument instead.")
         with self.assertWarnsWith(DeprecationWarning, msg):
             self.nwbfile.add_scratch(name='test', data=[1, 2, 3, 4, 5], notes='test notes')
         self.assertEqual(self.nwbfile.scratch['test'].description, 'test notes')    
 
     def test_add_scratch_table_description_deprecation(self):
-        msg =  ("Use of the `notes` or `table_description` argument is deprecated. "
-                "Use the `description` argument instead.")
+        msg =  ('Use of the `notes` or `table_description` argument is deprecated and will be removed in PyNWB 4.0. '
+                'Use the `description` argument instead.')
         df = pd.DataFrame(data={'col1': [1, 2, 3, 4], 'col2': ['a', 'b', 'c', 'd']})
         with self.assertWarnsWith(DeprecationWarning, msg):
             self.nwbfile.add_scratch(name='test', data=df,