Motivation

Fix #2008. Upgrades PendingDeprecationWarnings to DeprecationWarnings and upgrades DeprecationWarnings to raise ValueErrors when creating new objects or UserWarnings on read. Also removes functions previously marked for deprecation.

Here is a summary of the classes and methods updated:

• 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 ec_electrodes property is replaced by 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
• ImagingPlane.conversion will be deprecated in favor of origin coords and grid_spacing
• IndexSeries.unit is fixed
• Indexed_timeseries replaced by indexed_images
• _get_resources was removed
• NWBFile.modules is replaced by NWBFile.processing

TODO

• target the release-3.0 branch before merging (?)
• instead of raising UserWarnings for deprecated types on read, we discussed offline about not raising any warnings on read. A user working with older files using deprecated types will likely not be able to do anything to address the presence of deprecated types.

Checklist

• Did you update CHANGELOG.md with your changes?
• Have you checked our Contributing document?
• Have you ensured the PR clearly describes the problem and the solution?
• Is your contribution compliant with our coding style? This can be checked running ruff check . && codespell from the source directory.
• Have you checked to ensure that there aren't other open Pull Requests for the same change?
• Have you included the relevant issue number using "Fix #XXX" notation where XXX is the issue number? By including "Fix #XXX" you allow GitHub to close issue #XXX when the PR is merged.