[Feature]: Update deprecations for pynwb 3.0

[stephprince]

What would you like to see added to PyNWB?

For the pynwb 3.0 major release, we plan to raise errors instead of warnings when creating new objects using deprecated classes or using deprecated methods. Deprecated types will still be able to be read.

What solution would you like?

This issue compiles a list of the classes and methods to update:

• ProcessingModule.add_container will be replaced by ProcessingModule.add
• ProcessingModule.get_container will be replaced by ProcessingModule.get
• ProcessingModule.add_data_interface will be replaced by ProcessingModule.add
• ProcessingModule.get_data_interface will be replaced by ProcessingModule.get
• ScratchData.notes will be replaced by ScratchData.description
• Clustering will raise an error when creating a new object.
• ClusterWaveforms will raise an error when creating a new object.
• /intracellular_ephys/filtering will raise an error when creating a new object.
• NWBFile arg ic_electrodes will be replaced by arg icephys_electrodes
• NWBFile.add_ic_electrode, NWBFile.create_ic_electrode, and NWBFile.get_ic_electrode will be removed
• NWBFile.add_epoch_metadata_column will be removed
• SweepTable will raise an error when creating a new object and functions that interacted with the SweepTable will be modified
• ImageSeries.bits_per_pixel will be removed
• ImageSeries.format changed to external, default value for format should raise Value error
• ImagingPlane.manifold will raise an error when creating a new object
• IndexSeries.unit is fixed
• Indexed_timeseries replaced by indexed_images

Do you have any interest in helping implement the feature?

Yes.

Code of Conduct

• I agree to follow this project's Code of Conduct
• Have you checked the Contributing document?
• Have you ensured this change was not already requested?

[t-b]

Is there consensus already what the behaviour of pynwb 3.0 will be regarding reading of pynwb 2.x files? Or to rephrase will pynwb 3.x support reading files from pynwb 2.x (or compliant)?

[stephprince]

@t-b I realized the phrasing of the issue was inaccurate and have updated it. To clarify, we plan to guarantee that we can read all NWB 2.0 files with pynwb 3.x but will not allow the creation of new NWB data with deprecated types.

[t-b]

@stephprince Thanks Steph. I appreciate the rewording. And of course the fact that 2.x files can still be read.

A related topic is that I would appreciate a alpha/beta/rc release before the final one, for testing.