Add PyNWB 3.0 support

[stephprince]

Motivation

Address deprecations and validation changes in the upcoming PyNWB 3.0 release.

Note: I left some remaining TODO items that can be updated after the official release when 3.0 becomes the new minimum for NWBInspector.

To test:

cd nwbinspector
pip install -e . 
pip install pynwb==3.0.0rc1
pytest

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 75.00000% with 1 line in your changes missing coverage. Please review.

Project coverage is 86.73%. Comparing base (33ca373) to head (3fee92f).

Files with missing lines	Patch %	Lines
src/nwbinspector/_nwb_inspection.py	75.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##              dev     #557      +/-   ##
==========================================
+ Coverage   82.73%   86.73%   +3.99%     
==========================================
  Files          47       47              
  Lines        1512     1515       +3     
==========================================
+ Hits         1251     1314      +63     
+ Misses        261      201      -60     

Files with missing lines	Coverage Δ
src/nwbinspector/checks/_images.py	91.30% <ø> (ø)
src/nwbinspector/_nwb_inspection.py	86.95% <75.00%> (+3.99%)	⬆️

... and 4 files with indirect coverage changes

[rly]

Do you have any idea why the streaming tests are taking more than 1h 45m?

[stephprince]

I'm not sure, I just noticed that. I can cancel the run for now and try to debug locally?

[rly]

Sounds good.

Also, some time ago we had unofficially decided that NWB Zarr files should have the suffix ".nwb.zarr". I think we should keep that. NeurodataWithoutBorders/pynwb#1976 (comment) . NWB HDF5 files should still have suffix ".nwb" though. It can have the "hdf5" part before then to be explicit in these tests if we want.

[stephprince]

Also, some time ago we had unofficially decided that NWB Zarr files should have the suffix ".nwb.zarr". I think we should keep that.

Ah right, thanks for catching. I was modifying the tests to address the new NWBHDF5IO warning to use the .nwb extension and forgot the recommendation was .nwb.zarr for Zarr files. I will fix those names.