Upgrade validation methods

NeurodataWithoutBorders / pynwb

A Python API for working with Neurodata stored in the NWB Format

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Motivation

Addresses several issues summarized in #1808. This is a breaking change for the next major release.

fix #1807 so that validate returns the same output whether paths or io is provided
fix #1756 by adding a pynwb-validate entry point
fix #1179 by adding the option to output the validator output to a json file
fix #1953 by moving the CLI to a separate file, allowing the user to run python -m pynwb.validation_cli "test.nwb" as an alternative to the entry point
fix #1530 by updating the documentation and adding notes to the validate and validation cli docstrings to point users to NWB inspector
partially address #1493 by moving pynwb.validate into pynwb.validation module so that validate is the function name and validation is the module name

This PR also modifies the validate method so that it

accepts a single path as input (the CLI still accepts multiple paths)
no longer returns a status code but will return errors if the function fails in the process of performing validation. (The CLI still returns an exit code).

TODO

[ ] finish testing with ZarrIO
[X] test with nwbinspector (as of now should only require changes to this line)
[x] check test coverage
[ ] when publishing the next release on conda-forge, the recipe file should also be updated to add the pynwb-validate entry point

Checklist

[x] Did you update CHANGELOG.md with your changes?
[x] Have you checked our Contributing document?
[x] Have you ensured the PR clearly describes the problem and the solution?
[x] Is your contribution compliant with our coding style? This can be checked running flake8 from the source directory.
[x] Have you checked to ensure that there aren't other open Pull Requests for the same change?
[x] 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.

Codecov Report

Attention: Patch coverage is 45.00000% with 66 lines in your changes missing coverage. Please review.

Project coverage is 82.25%. Comparing base (a63387d) to head (12bc84c).

Files with missing lines	Patch %	Lines
src/pynwb/validation_cli.py	0.00%	41 Missing :warning:
src/pynwb/validation.py	67.16%	15 Missing and 7 partials :warning:
src/pynwb/__init__.py	75.00%	2 Missing and 1 partial :warning:

Files with missing lines

Patch %

Lines

src/pynwb/validation_cli.py

0.00%

41 Missing :warning:

src/pynwb/validation.py

67.16%

15 Missing and 7 partials :warning:

src/pynwb/__init__.py

75.00%

2 Missing and 1 partial :warning:

:exclamation: There is a different number of reports uploaded between BASE (a63387d) and HEAD (12bc84c). Click for more details.

HEAD has 7 uploads less than BASE

| Flag | BASE (a63387d) | HEAD (12bc84c) | |------|------|------| |unit|4|1| |integration|4|0|

Additional details and impacted files

```diff @@ Coverage Diff @@ ## dev #1911 +/- ## ========================================== - Coverage 91.88% 82.25% -9.64% ========================================== Files 27 28 +1 Lines 2711 2733 +22 Branches 707 708 +1 ========================================== - Hits 2491 2248 -243 - Misses 144 381 +237 - Partials 76 104 +28 ``` | [Flag](https://app.codecov.io/gh/NeurodataWithoutBorders/pynwb/pull/1911/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=NeurodataWithoutBorders) | Coverage Δ | | |---|---|---| | [integration](https://app.codecov.io/gh/NeurodataWithoutBorders/pynwb/pull/1911/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=NeurodataWithoutBorders) | `?` | | | [unit](https://app.codecov.io/gh/NeurodataWithoutBorders/pynwb/pull/1911/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=NeurodataWithoutBorders) | `82.25% <45.00%> (-0.60%)` | :arrow_down: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=NeurodataWithoutBorders#carryforward-flags-in-the-pull-request-comment) to find out more.

NeurodataWithoutBorders / pynwb