Upgrade validation methods - make pynwb.validate behave similarly for io and paths

[stephprince]

Motivation

Address #1807 (related to other validation upgrades described in #1808). This is a breaking change for the next major release.

The expected behavior is for validate to return the same output whether paths or io is provided. This was previously discussed here, where the 'correct' behavior for the example below is to return: "The namespace 'core' is included by the namespace 'ndx-testextension'. Please validate against that namespace instead".

How to test the behavior?

import h5py
from pynwb.validate import validate
from pynwb import NWBHDF5IO

path = 'tests/back_compat/2.1.0_nwbfile_with_extension.nwb'
io = NWBHDF5IO('tests/back_compat/2.1.0_nwbfile_with_extension.nwb')

print('Validating all with paths')
validate(paths=[path], namespace="core", verbose=True)

print('Validating core with io')
validate(io=io, namespace="core", verbose=True)

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 flake8 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.

[stephprince]

I wasn't sure if there is a better way to load the namespaces from the io object, I realize this is HDF5 specific, but it looks like the original namespace loading was as well? I was wondering how this works for Zarr validation?

[stephprince]

I'm not sure if all of these are necessary to include, but wanted to double check they were all equivalent

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 92.00%. Comparing base (04a6506) to head (76a4f0f).

Additional details and impacted files

@@            Coverage Diff             @@
##              dev    #1911      +/-   ##
==========================================
+ Coverage   91.88%   92.00%   +0.11%     
==========================================
  Files          27       27              
  Lines        2651     2663      +12     
  Branches      692      694       +2     
==========================================
+ Hits         2436     2450      +14     
+ Misses        142      141       -1     
+ Partials       73       72       -1     

Flag	Coverage Δ
integration	73.07% <100.00%> (+0.27%)	⬆️
unit	83.92% <44.89%> (-0.05%)	⬇️

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

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[stephprince]

from what I could tell, this status check was never reset to 0, so if any of the paths return a nonzero status, _validate_helper would not be run on any subsequent paths. Is that the intended behavior? Or maybe I am misunderstanding something.