Generalize Validation

[CodyCBakerPhD]

fix #1431
replaces #1494 by branching from dev instead of the modularity improvement

Motivation

WIP synchronizing the behavior of the CLI pynwb.validate function with the library-imported one, namely for the purposes of validating against cached namespaces (but also just to have identical behavior between library and CLI use cases).

How to test the behavior?

Need to...

• Thoroughly test that the CLI usage behaves as it used to
• The cached namespace feature is indeed available to the new library method as well
• Ensure there is no break in back-combability when using the previous methods

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? - a splinter/extension of enh/getcachednamespaces
• 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.

[rly]

Ah, looks like you are still working on this. Happy to help or review it when ready.

[CodyCBakerPhD]

@rly @oruebel This is ready to be looked at...

Main issue I'm having right now is getting the non-required argument parsing through docval to work.

Traceback (most recent call last):
  File "C:\Users\Raven\.conda\envs\pynwb\lib\runpy.py", line 194, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "C:\Users\Raven\.conda\envs\pynwb\lib\runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "d:\github\pynwb\src\pynwb\validate.py", line 223, in <module>
    validate_cli()
  File "d:\github\pynwb\src\pynwb\validate.py", line 213, in validate_cli
    validation_errors, validation_status = validate(
  File "C:\Users\Raven\.conda\envs\pynwb\lib\site-packages\hdmf\utils.py", line 648, in func_call
    pargs = _check_args(args, kwargs)
  File "C:\Users\Raven\.conda\envs\pynwb\lib\site-packages\hdmf\utils.py", line 637, in _check_args
    raise ExceptionType(msg)
TypeError: validate: incorrect type for 'namespace' (got 'NoneType', expected 'str or NoneType')

[CodyCBakerPhD]

but likewise if I remove the type: (..., type(None)) to mimic the pattern of https://github.com/NeurodataWithoutBorders/pynwb/blob/dev/src/pynwb/image.py#L38-L43 I still get

Traceback (most recent call last):
  File "C:\Users\Raven\.conda\envs\pynwb\lib\runpy.py", line 194, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "C:\Users\Raven\.conda\envs\pynwb\lib\runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "d:\github\pynwb\src\pynwb\validate.py", line 223, in <module>
    validate_cli()
  File "d:\github\pynwb\src\pynwb\validate.py", line 213, in validate_cli
    validation_errors, validation_status = validate(
  File "C:\Users\Raven\.conda\envs\pynwb\lib\site-packages\hdmf\utils.py", line 648, in func_call
    pargs = _check_args(args, kwargs)
  File "C:\Users\Raven\.conda\envs\pynwb\lib\site-packages\hdmf\utils.py", line 637, in _check_args
    raise ExceptionType(msg)
TypeError: validate: incorrect type for 'namespace' (got 'NoneType', expected 'str')

[CodyCBakerPhD]

Main issue I'm having right now is getting the non-required argument parsing through docval to work.

Never mind, I just had to set the CLI parser default value to resolve this.

[CodyCBakerPhD]

@rly @oruebel Now I'm trying to debug these failing validation CLI tests, but when I locally run the tests it gives

   .... Massive stack trace....
               FileNotFoundError: [Errno 2] No such file or directory: 'coverage'

How do I obtain this 'coverage' folder with what I presume contains NWB files I need to test against?

[codecov]

Codecov Report

Merging #1511 (06ca152) into dev (6e1f131) will increase coverage by 0.68%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##              dev    #1511      +/-   ##
==========================================
+ Coverage   90.65%   91.34%   +0.68%     
==========================================
  Files          25       25              
  Lines        2494     2507      +13     
  Branches      466      471       +5     
==========================================
+ Hits         2261     2290      +29     
+ Misses        148      137      -11     
+ Partials       85       80       -5     

Flag	Coverage Δ
integration	70.56% <100.00%> (+0.95%)	⬆️
unit	84.44% <24.71%> (+0.28%)	⬆️

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

Impacted Files	Coverage Δ
src/pynwb/__init__.py	76.15% <100.00%> (-1.22%)	⬇️
src/pynwb/validate.py	100.00% <100.00%> (+21.05%)	⬆️

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[rly]

Coverage on the new validate.py is now 100%. Woot!

[oruebel]

Thanks @CodyCBakerPhD and @rly for all the work on this PR to clean up validation!