Update deprecations

CHANGELOG.md

@@ -2,6 +2,11 @@
 
 ## PyNWB 3.0.0 (Upcoming)
 
+### Deprecations
+- The following deprecated classes will now raise errors when creating new instances of these classes: ClusteringWaveforms, Clustering, SweepTable. Reading files using these data types will continue to be supported.
+- The following methods and arguments have been deprecated: ProcessingModule.add_container, ProcessingModule.get_container, ProcessingModule.add_data_interface, ProcessingModule.get_data_interface, ScratchData.notes, NWBFile.ic_electrodes, NWBFile.ec_electrodes, NWBFile.icephys_filtering, NWBFile.modules, ImageSeries.bits_per_pixel, ImageSeries.format, ImagingPlane.manifold, ImagingPlane.conversion, IndexSeries.unit, IndexSeries.indexed_timeseries
+- The following deprecated methods have been removed: NWBFile.add_ic_electrode, NWBFile.create_ic_electrode, NWBFile.get_ic_electrode, pynwb._get_resources
+
 ### Enhancements and minor changes
 - Added support for NWB schema 2.8.0. @rly [#2001](https://github.com/NeurodataWithoutBorders/pynwb/pull/2001)
   - Removed `SpatialSeries.bounds` field that was not functional. This will be fixed in a future release. @rly [#1907](https://github.com/NeurodataWithoutBorders/pynwb/pull/1907), [#1996](https://github.com/NeurodataWithoutBorders/pynwb/pull/1996)

docs/gallery/general/scratch.py

@@ -145,7 +145,7 @@
 # Now lets do an analysis for which we do not have a specification, but we would like to store
 # the results for.
 
-filt_ts = nwb_scratch.modules["filtering_module"]["filtered_timeseries"]
+filt_ts = nwb_scratch.processing["filtering_module"]["filtered_timeseries"]
 
 fft = np.fft.fft(filt_ts.data)
 

src/pynwb/__init__.py

@@ -79,12 +79,6 @@ def __get_resources() -> dict:
     return ret
 
 
-def _get_resources():
-    # LEGACY: Needed to support legacy implementation.
-    # TODO: Remove this in PyNWB 3.0.
-    warn("The function '_get_resources' is deprecated and will be removed in a future release.", DeprecationWarning)
-    return __get_resources()
-
 
 # a global type map
 global __TYPE_MAP

src/pynwb/base.py

@@ -50,26 +50,25 @@ def add_container(self, **kwargs):
         '''
         Add an NWBContainer to this ProcessingModule
         '''
-        warn(PendingDeprecationWarning('add_container will be replaced by add'))
+        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):
         '''
         Retrieve an NWBContainer from this ProcessingModule
         '''
-        warn(PendingDeprecationWarning('get_container will be replaced by get'))
+        warn('get_container is deprecated. Use get instead.', DeprecationWarning)
         return self.get(kwargs['container_name'])
 
     @docval({'name': 'NWBDataInterface', 'type': (NWBDataInterface, DynamicTable),
              'doc': 'the NWBDataInterface to add to this Module'})
     def add_data_interface(self, **kwargs):
-        warn(PendingDeprecationWarning('add_data_interface will be replaced by add'))
-        self.add(kwargs['NWBDataInterface'])
+        warn('add_data_interface is deprecated. Use add instead.', DeprecationWarning)
 
     @docval({'name': 'data_interface_name', 'type': str, 'doc': 'the name of the NWBContainer to retrieve'})
     def get_data_interface(self, **kwargs):
-        warn(PendingDeprecationWarning('get_data_interface will be replaced by get'))
+        warn('get_data_interface is deprecated. Use get instead.', DeprecationWarning)
         return self.get(kwargs['data_interface_name'])
 
 

src/pynwb/core.py

@@ -128,27 +128,27 @@ def __init__(self, **kwargs):
         notes, description = popargs('notes', 'description', kwargs)
         super().__init__(**kwargs)
         if notes != '':
-            warn('The `notes` argument of ScratchData.__init__ will be deprecated. Use description instead.',
-                 PendingDeprecationWarning)
-            if notes != '' and description != '':
+            self._error_on_new_warn_on_construct(
+                    error_msg=("The `notes` argument of ScratchData.__init__ has been deprecated. "
+                               "Use description instead.")
+                    )
+            if notes != '' and description is not None:
                 raise ValueError('Cannot provide both notes and description to ScratchData.__init__. The description '
                                  'argument is recommended.')
             description = notes
         if not description:
-            warn('ScratchData.description will be required in a future major release of PyNWB.',
-                 PendingDeprecationWarning)
+            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 will be deprecated. Use ScratchData.description instead.',
-             PendingDeprecationWarning)
+        warn('Use of ScratchData.notes has been deprecated. Use ScratchData.description instead.', DeprecationWarning)
         return self.description
-
+    
     @notes.setter
     def notes(self, value):
-        warn('Use of ScratchData.notes will be deprecated. Use ScratchData.description instead.',
-             PendingDeprecationWarning)
+        self._error_on_new_warn_on_construct(
+                    error_msg='Use of ScratchData.notes has been deprecated. Use ScratchData.description instead.')
         self.description = value
 
 

src/pynwb/ecephys.py

@@ -227,7 +227,9 @@ class Clustering(NWBDataInterface):
              'shape': (None,)},
             {'name': 'name', 'type': str, 'doc': 'the name of this container', 'default': 'Clustering'})
     def __init__(self, **kwargs):
-        warnings.warn("use pynwb.misc.Units or NWBFile.units instead", DeprecationWarning)
+        self._error_on_new_warn_on_construct(
+            error_msg='The Clustering neurodata type is deprecated. Use pynwb.misc.Units or NWBFile.units instead'
+        )
         args_to_set = popargs_to_dict(('description', 'num', 'peak_over_rms', 'times'), kwargs)
         super().__init__(**kwargs)
         args_to_set['peak_over_rms'] = list(args_to_set['peak_over_rms'])
@@ -261,7 +263,9 @@ class ClusterWaveforms(NWBDataInterface):
              'doc': 'the standard deviations of waveforms for each cluster'},
             {'name': 'name', 'type': str, 'doc': 'the name of this container', 'default': 'ClusterWaveforms'})
     def __init__(self, **kwargs):
-        warnings.warn("use pynwb.misc.Units or NWBFile.units instead", DeprecationWarning)
+        self._error_on_new_warn_on_construct(
+            error_msg='The ClusterWaveforms neurodata type is deprecated. Use pynwb.misc.Units or NWBFile.units instead'
+        )
         args_to_set = popargs_to_dict(('clustering_interface', 'waveform_filtering',
                                        'waveform_mean', 'waveform_sd'), kwargs)
         super().__init__(**kwargs)

src/pynwb/file.py

@@ -384,7 +384,8 @@ class NWBFile(MultiContainerInterface, HERDManager):
              'doc': 'DEPRECATED use icephys_electrodes parameter instead. '
                     'IntracellularElectrodes that belong to this NWBFile', 'default': None},
             {'name': 'sweep_table', 'type': SweepTable,
-             'doc': 'the SweepTable that belong to this NWBFile', 'default': None},
+             'doc': '[DEPRECATED] Use IntracellularRecordingsTable instead. '
+                    'The SweepTable that belong to this NWBFile', 'default': None},
             {'name': 'imaging_planes', 'type': (list, tuple),
              'doc': 'ImagingPlanes that belong to this NWBFile', 'default': None},
             {'name': 'ogen_sites', 'type': (list, tuple),
@@ -491,11 +492,17 @@ def __init__(self, **kwargs):
         icephys_electrodes = args_to_set['icephys_electrodes']
         ic_electrodes = args_to_set['ic_electrodes']
         if icephys_electrodes is None and ic_electrodes is not None:
-            warn("Use of the ic_electrodes parameter is deprecated. "
-                 "Use the icephys_electrodes parameter instead", DeprecationWarning)
+            self._error_on_new_warn_on_construct(error_msg=("Use of the ic_electrodes parameter is deprecated. "
+                                                            "Use the icephys_electrodes parameter instead"))
             args_to_set['icephys_electrodes'] = ic_electrodes
         args_to_set.pop('ic_electrodes')  # do not set this arg
 
+        # backwards-compatibility for sweep table
+        if args_to_set['sweep_table'] is not None:
+            self._error_on_new_warn_on_construct(error_msg=("SweepTable is deprecated. Use the "
+                                                            "IntracellularRecordingsTable instead. See also the "
+                                                            "NWBFile.add_intracellular_recordings function."))
+
         # convert single experimenter to tuple
         experimenter = args_to_set['experimenter']
         if isinstance(experimenter, str):
@@ -552,7 +559,7 @@ def objects(self):
 
     @property
     def modules(self):
-        warn("NWBFile.modules has been replaced by NWBFile.processing.", DeprecationWarning)
+        self._error_on_new_warn_on_construct(error_msg="NWBFile.modules is deprecated. Use NWBFile.processing instead.")
         return self.processing
 
     @property
@@ -561,17 +568,20 @@ def epoch_tags(self):
 
     @property
     def ec_electrode_groups(self):
-        warn("NWBFile.ec_electrode_groups has been replaced by NWBFile.electrode_groups.", DeprecationWarning)
+        self._error_on_new_warn_on_construct(error_msg=("NWBFile.ec_electrode_groups is deprecated. "
+                                                        "Use NWBFile.electrode_groups instead."))
         return self.electrode_groups
 
     @property
     def ec_electrodes(self):
-        warn("NWBFile.ec_electrodes has been replaced by NWBFile.electrodes.", DeprecationWarning)
+        self._error_on_new_warn_on_construct(error_msg=("NWBFile.ec_electrodes is deprecated. "
+                                                        "Use NWBFile.electrodes instead."))
         return self.electrodes
 
     @property
     def ic_electrodes(self):
-        warn("NWBFile.ic_electrodes has been replaced by NWBFile.icephys_electrodes.", DeprecationWarning)
+        self._error_on_new_warn_on_construct(error_msg=("NWBFile.ic_electrodes is deprecated. "
+                                                        "Use NWBFile.icephys_electrodes instead."))
         return self.icephys_electrodes
 
     @property
@@ -581,34 +591,10 @@ def icephys_filtering(self):
     @icephys_filtering.setter
     def icephys_filtering(self, val):
         if val is not None:
-            warn("Use of icephys_filtering is deprecated. Use the IntracellularElectrode.filtering field instead",
-                 DeprecationWarning)
+            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 add_ic_electrode(self, *args, **kwargs):
-        """
-        This method is deprecated and will be removed in future versions. Please
-        use :py:meth:`~pynwb.file.NWBFile.add_icephys_electrode` instead
-        """
-        warn("NWBFile.add_ic_electrode has been replaced by NWBFile.add_icephys_electrode.", DeprecationWarning)
-        return self.add_icephys_electrode(*args, **kwargs)
-
-    def create_ic_electrode(self, *args, **kwargs):
-        """
-        This method is deprecated and will be removed in future versions. Please
-        use :py:meth:`~pynwb.file.NWBFile.create_icephys_electrode` instead
-        """
-        warn("NWBFile.create_ic_electrode has been replaced by NWBFile.create_icephys_electrode.", DeprecationWarning)
-        return self.create_icephys_electrode(*args, **kwargs)
-
-    def get_ic_electrode(self, *args, **kwargs):
-        """
-        This method is deprecated and will be removed in future versions. Please
-        use :py:meth:`~pynwb.file.NWBFile.get_icephys_electrode` instead
-        """
-        warn("NWBFile.get_ic_electrode has been replaced by NWBFile.get_icephys_electrode.", DeprecationWarning)
-        return self.get_icephys_electrode(*args, **kwargs)
-
     def __check_epochs(self):
         if self.epochs is None:
             self.epochs = TimeIntervals(name='epochs', description='experimental epochs')
@@ -622,13 +608,6 @@ def add_epoch_column(self, **kwargs):
         self.__check_epochs()
         self.epochs.add_column(**kwargs)
 
-    def add_epoch_metadata_column(self, *args, **kwargs):
-        """
-        This method is deprecated and will be removed in future versions. Please
-        use :py:meth:`~pynwb.file.NWBFile.add_epoch_column` instead
-        """
-        raise DeprecationWarning("Please use NWBFile.add_epoch_column")
-
     @docval(*get_docval(TimeIntervals.add_interval),
             allow_extra=True)
     def add_epoch(self, **kwargs):
@@ -837,7 +816,12 @@ def _check_sweep_table(self):
         Create a SweepTable if not yet done.
         """
         if self.sweep_table is None:
-            self.sweep_table = SweepTable(name='sweep_table')
+            if self._in_construct_mode:
+                sweep_table = SweepTable.__new__(SweepTable, parent=self, in_construct_mode=True)
+                sweep_table.__init__(name='sweep_table')
+            else:
+                sweep_table = SweepTable(name='sweep_table')
+            self.sweep_table = sweep_table
 
     def _update_sweep_table(self, nwbdata):
         """
@@ -860,23 +844,11 @@ def add_acquisition(self, **kwargs):
 
     @docval({'name': 'stimulus', 'type': (TimeSeries, DynamicTable, NWBDataInterface), 'default': None,
              'doc': 'The stimulus presentation data to add to this NWBFile.'},
-            {'name': 'use_sweep_table', 'type': bool, 'default': False, 'doc': 'Use the deprecated SweepTable'},
-            {'name': 'timeseries', 'type': TimeSeries, 'default': None,
-             'doc': 'The "timeseries" keyword argument is deprecated. Use the "nwbdata" argument instead.'},)
+            {'name': 'use_sweep_table', 'type': bool, 'default': False, 'doc': 'Use the deprecated SweepTable'},)
     def add_stimulus(self, **kwargs):
-        stimulus, timeseries = popargs('stimulus', 'timeseries', kwargs)
-        if stimulus is None and timeseries is None:
-            raise ValueError(
-                "The 'stimulus' keyword argument is required. The 'timeseries' keyword argument can be "
-                "provided for backwards compatibility but is deprecated in favor of 'stimulus' and will be "
-                "removed in PyNWB 3.0."
-            )
-        # TODO remove this support in PyNWB 3.0
-        if timeseries is not None:
-            warn("The 'timeseries' keyword argument is deprecated and will be removed in PyNWB 3.0. "
-                 "Use the 'stimulus' argument instead.", DeprecationWarning)
-            if stimulus is None:
-                stimulus = timeseries
+        stimulus = popargs('stimulus', kwargs)
+        if stimulus is None:
+            raise ValueError("The 'stimulus' keyword argument is required.")
         self._add_stimulus_internal(stimulus)
         use_sweep_table = popargs('use_sweep_table', kwargs)
         if use_sweep_table:
@@ -1061,11 +1033,12 @@ def get_icephys_meta_parent_table(self):
              'doc': 'The name of the data. Required only when passing in a scalar, numpy.ndarray, list, or tuple',
              'default': None},
             {'name': 'notes', 'type': str,
-             'doc': ('Notes to add to the data. Only used when passing in numpy.ndarray, list, or tuple. This '
-                     'argument is not recommended. Use the `description` argument instead.'),
+             'doc': ('[DEPRECATED] Notes to add to the data. '
+                     'Only used when passing in numpy.ndarray, list, or tuple. This argument is not recommended. '
+                     'Use the `description` argument instead.'),
              'default': None},
             {'name': 'table_description', 'type': str,
-             'doc': ('Description for the internal DynamicTable used to store a pandas.DataFrame. This '
+             'doc': ('[DEPRECATED] Description for the internal DynamicTable used to store a pandas.DataFrame. This '
                      'argument is not recommended. Use the `description` argument instead.'),
              'default': ''},
             {'name': 'description', 'type': str,
@@ -1078,8 +1051,8 @@ 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 will be removed in a future version of PyNWB. '
-                 'Use the `description` argument instead.', PendingDeprecationWarning)
+            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')
 

src/pynwb/icephys.py

@@ -338,9 +338,12 @@ class SweepTable(DynamicTable):
              'default': "A sweep table groups different PatchClampSeries together."},
             *get_docval(DynamicTable.__init__, 'id', 'columns', 'colnames'))
     def __init__(self, **kwargs):
-        warnings.warn("Use of SweepTable is deprecated. Use the IntracellularRecordingsTable "
-                      "instead. See also the  NWBFile.add_intracellular_recordings function.",
-                      DeprecationWarning)
+        error_msg=('SweepTable is deprecated. Use the IntracellularRecordingsTable instead. '
+                   'See also the NWBFile.add_intracellular_recordings function.')
+        if not self._in_construct_mode:
+            raise ValueError(error_msg)
+        warnings.warn(error_msg)
+
         super().__init__(**kwargs)
 
     @docval({'name': 'pcs', 'type': PatchClampSeries,