Change: Only embed specs/namespaces for types that are included in NWB file on export

[ehennestad]

Fix #607

Motivation

Ensure that only relevant namespaces/specifications are embedded in an NWB file. This issue suggests that such extra namespaces can cause errors when validating with NWBInspector.

How to test the behavior?

Export NWB file with types from a subset of available extension and check the file's `specification` group

Questions / todo

• Are namespace names always specified in kebab-case? - Appears so
•  Does matnwb always format namespace names as snake_case? - Appears so
• Should the specification group be completely cleared before rewriting it if exporting to an existing file?
• Check superclasses of each type and included namespace of superclasses as well
• Add unit test

Checklist

• Have you ensured the PR description clearly describes the problem and solutions?
• Have you checked to ensure that there aren't other open or previously closed Pull Requests for the same change?
• If this PR fixes an issue, is the first line of the PR description fix #XX where XX is the issue number?

[codecov]

Codecov Report

Attention: Patch coverage is 92.68293% with 9 lines in your changes missing coverage. Please review.

Project coverage is 95.19%. Comparing base (ab53589) to head (ab79e41).

Files with missing lines	Patch %	Lines
+io/+internal/+h5/mustBeH5File.m	55.55%	4 Missing ⚠️
+io/+internal/+h5/mustBeH5FileReference.m	66.66%	2 Missing ⚠️
+io/+internal/+h5/resolveFileReference.m	87.50%	1 Missing ⚠️
+schemes/+utility/listNwbTypeHierarchy.m	87.50%	1 Missing ⚠️
NwbFile.m	96.87%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #615      +/-   ##
==========================================
+ Coverage   95.18%   95.19%   +0.01%     
==========================================
  Files         124      137      +13     
  Lines        5045     5165     +120     
==========================================
+ Hits         4802     4917     +115     
- Misses        243      248       +5     

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[bendichter]

I don't think it's a big deal that way this is used here, but note that deleting groups and datasets from an HDF5 file does not free up the space

[bendichter]

There are lots of new functions here that lack unit tests