Update deprecations (#2011)

* update deprecated classes and methods * update deprecation warnings * update tests for deprecated classes and functions * fix warnings and formatting * add scratch tests and deprecations * keep function behavior for deprecation warnings * update CHANGELOG.md * add tests for deprecations * update scratch tutorial * skip deprecated gallery examples * update CHANGELOG.md * remove old icephys tutorial * add pynwb 4.0 deprecation info * add error on new pass on construct method * remove warnings on construct for deprecations * fix formatting * update hdmf-zarr url * Apply suggestions from code review Co-authored-by: Ryan Ly <[email protected]> * Update src/pynwb/core.py Co-authored-by: Ryan Ly <[email protected]> * add code review suggestions * add catch for extra warning * remove unused variable --------- Co-authored-by: Ryan Ly <[email protected]>
NeurodataWithoutBorders · Dec 23, 2024 · e47cd5a · e47cd5a
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,27 @@
 
 ## 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`` and ``ProcessingModule.add_data_interface`` are replaced by  ``ProcessingModule.add``
+  - ``ProcessingModule.get_container`` and ``ProcessingModule.get_data_interface`` are replaced by ``ProcessingModule.get``
+  - ``ScratchData.notes`` is deprecated. Use ``ScratchData.description`` instead.
+  - ``NWBFile.ic_electrodes`` is deprecated. Use ``NWBFile.icephys_electrodes`` instead.
+  - ``NWBFile.ec_electrodes`` is deprecated. Use ``NWBFile.electrodes`` instead.
+  - ``NWBFile.icephys_filtering`` is deprecated. Use ``IntracellularElectrode.filtering`` instead.
+  - ``NWBFile.modules`` is deprecated. Use ``NWBFile.processing`` instead.
+  - ``ImageSeries.format`` is fixed to 'external' if an external file is provided.
+  - ``ImageSeries.bits_per_pixel`` is deprecated.
+  - ``ImagingPlane.manifold``, ``ImagingPlane.conversion`` and ``ImagingPlane.unit`` are deprecated. Use ``ImagingPlane.origin_coords`` and ``ImagingPlane.grid_spacing`` instead.
+  - ``IndexSeries.unit`` is fixed to "N\A". 
+  - ``IndexSeries.indexed_timeseries`` is deprecated. Use ``IndexSeries.indexed_images`` instead.
+- The following deprecated methods have been removed:
+  - ``NWBFile.add_ic_electrode`` is removed. Use ``NWBFile.add_icephys_electrode`` instead.
+  - ``NWBFile.create_ic_electrode`` is removed. Use ``NWBFile.create_icephys_electrode`` instead.
+  - ``NWBFile.get_ic_electrode`` is removed. Use ``NWBFile.get_icephys_electrode`` instead.
+  - ``pynwb._get_resources`` is removed.
+
 ### 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)

diff --git a/docs/gallery/domain/icephys.py b/docs/gallery/domain/icephys.py
diff --git a/docs/gallery/general/scratch.py b/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)
 

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -148,7 +148,7 @@ def __call__(self, filename):
     'nwbwidgets': ("https://nwb-widgets.readthedocs.io/en/latest/", None),
     'nwb-overview': ("https://nwb-overview.readthedocs.io/en/latest/", None),
     'zarr': ("https://zarr.readthedocs.io/en/stable/", None),
-    'hdmf-zarr': ("https://hdmf-zarr.readthedocs.io/en/latest/", None),
+    'hdmf-zarr': ("https://hdmf-zarr.readthedocs.io/en/stable/", None),
     'numcodecs': ("https://numcodecs.readthedocs.io/en/latest/", None),
 }
 
@@ -161,7 +161,7 @@ def __call__(self, filename):
     'hdmf-docs': ('https://hdmf.readthedocs.io/en/stable/%s', '%s'),
     'dandi': ('https://www.dandiarchive.org/%s', '%s'),
     "nwbinspector": ("https://nwbinspector.readthedocs.io/en/dev/%s", "%s"),
-    'hdmf-zarr': ('https://hdmf-zarr.readthedocs.io/en/latest/%s', '%s'),
+    'hdmf-zarr': ('https://hdmf-zarr.readthedocs.io/en/stable/%s', '%s'),
 }
 
 nitpicky = True

diff --git a/src/pynwb/__init__.py b/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

diff --git a/src/pynwb/base.py b/src/pynwb/base.py
@@ -51,26 +51,25 @@ 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 and will be removed in PyNWB 4.0. 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 and will be removed in PyNWB 4.0. 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 and will be removed in PyNWB 4.0. 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 and will be removed in PyNWB 4.0. Use get instead.', DeprecationWarning)
         return self.get(kwargs['data_interface_name'])