Use cached namespaces during validation

[stephprince]

Motivation

Fix #528.

Recent Zarr-related updates switched the inspector from using pynwb.validate(paths=paths) to pynwb.validate(io=io), resulting in the inspector not using cached namespaces during validation. We will temporarily revert this change, since pynwb validation of Zarr NWB files is not yet fully supported anyway due to pending issues that need to be addressed in hdmf/pynwb.

Since this is more of a bug on the pynwb side that using the io argument ignores the use_cached_namespaces=True setting in the validator (and will be updated in the next major pynwb release), I'm not sure if there are really any specific tests to add here.

While addressing this issue, I added a couple of other small updates to the Zarr support here:

1. Passing the path of an NWB file Zarr folder to the CLI (instead of the parent folder) would result in 0 files being inspected, due to some conditionals in inspect_all that detected whether the path provided was a directory of NWB files or an NWB file.
2. The test_inspect_all_parallel tests had been indented and were not running

[stephprince]

I'm not sure if (in_path / ".zgroup").exists() is the appropriate check here for a Zarr NWB file or if it is even necessary

[rly]

Can we use https://github.com/hdmf-dev/hdmf-zarr/blob/dev/src/hdmf_zarr/backend.py#L78 ?

[stephprince]

@rly you mentioned you had a related test file, can you let me know if this solves the issue or share the file?

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 86.71%. Comparing base (c26924b) to head (3efd7b8).

Additional details and impacted files

@@            Coverage Diff             @@
##              dev     #531      +/-   ##
==========================================
+ Coverage   82.77%   86.71%   +3.94%     
==========================================
  Files          47       47              
  Lines        1504     1506       +2     
==========================================
+ Hits         1245     1306      +61     
+ Misses        259      200      -59     

Files with missing lines	Coverage Δ
src/nwbinspector/_nwb_inspection.py	87.31% <100.00%> (+4.73%)	⬆️

... and 4 files with indirect coverage changes