Upgrade to Pydantic 2

[CodyCBakerPhD]

DANDI just finished the upgrade to Pydantic 2, so we need to keep up for our live service automatic upload + GUIDE bundling

Also fixes #662 by using typing_extensions.Self

[CodyCBakerPhD]

Just a minor readability change to the private methods; otherwise below there was a line that read as _find_location_in_memory_nwbfile(current_location=field_name) which looked weird until you followed the redirection and implicit logic enough to realize how the location is constructed recursively

[h-mayorquin]

Got you, this makes the signature more meaningful. Glad we make all of this private.

Should't the typing be NWBContainer? https://pynwb.readthedocs.io/en/stable/pynwb.core.html#pynwb.core.NWBContainer

[CodyCBakerPhD]

I think an NWBFile can have something that's a Container but not an NWBContainer? Maybe, maybe not - the typing and logic should apply to the most generic case however

[h-mayorquin]

This seems OK to me.

It is flattening the structure that we use to write the backend plus some minor changes that I agree with: field for dataset_name, creating another function for finding the location which has better signature semantics and making some properties class variables.

The most difficult thing is to read carefully through the test as the flattening of the structure implied that they have to change.

I also think that the diff in the tests resulted a bit larger than it had to be because we are testing string representations.

I will re-read the tests tomorrow just as a sanity check for my eyes and approve after as I think this is ready to go.

[h-mayorquin]

Got you, this makes the signature more meaningful. Glad we make all of this private.

Should't the typing be NWBContainer? https://pynwb.readthedocs.io/en/stable/pynwb.core.html#pynwb.core.NWBContainer

[codecov]

Codecov Report

Attention: Patch coverage is 93.84615% with 4 lines in your changes are missing coverage. Please review.

Project coverage is 91.08%. Comparing base (84ed29f) to head (beabed5).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #767      +/-   ##
==========================================
- Coverage   91.17%   91.08%   -0.10%     
==========================================
  Files         121      121              
  Lines        6315     6296      -19     
==========================================
- Hits         5758     5735      -23     
- Misses        557      561       +4     

Flag	Coverage Δ
unittests	91.08% <93.84%> (-0.10%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files	Coverage Δ
src/neuroconv/tools/nwb_helpers/__init__.py	100.00% <100.00%> (ø)
...nwb_helpers/_configuration_models/_base_backend.py	100.00% <100.00%> (ø)
...nwb_helpers/_configuration_models/_hdf5_backend.py	100.00% <100.00%> (ø)
..._helpers/_configuration_models/_hdf5_dataset_io.py	68.57% <100.00%> (-2.49%)	⬇️
...nwb_helpers/_configuration_models/_zarr_backend.py	100.00% <100.00%> (ø)
..._helpers/_configuration_models/_zarr_dataset_io.py	83.63% <100.00%> (-0.85%)	⬇️
.../neuroconv/tools/nwb_helpers/_configure_backend.py	95.23% <100.00%> (ø)
...roconv/tools/nwb_helpers/_dataset_configuration.py	91.66% <100.00%> (ø)
src/neuroconv/tools/testing/__init__.py	100.00% <ø> (ø)
...roconv/tools/testing/_mock/_mock_dataset_models.py	100.00% <100.00%> (ø)
... and 1 more

[h-mayorquin]

The tests look OK to me. This is good to go.

[h-mayorquin]

I guess that this is done by pydantic now.

[h-mayorquin]

mock at the beginning of the name. I think a good idea. It could also be mock_DatasetIOConfigurarion(backend: ["hdf5", "zarr"])) to save some code duplcation.

But I am not sure that is better and probably does not really matter for only two objects.