add NWBHDF5IO.read_nwb() method

[h-mayorquin]

This was discussed in #1974

This is the first part of the program described by @oruebel here. In a future PR and once hdmf-dev/hdmf-zarr#225 is merged I will implement pynwb.read_nwb in another PR.

Meanwhile, I have two questions:

1. What streaming method should be used when an s3 path is passed?
2. For testing this, the ros3 test have some files that I think I could use, is that OK?

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[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 91.92%. Comparing base (ad04661) to head (2ed4aa5).
Report is 1 commits behind head on dev.

Additional details and impacted files

@@            Coverage Diff             @@
##              dev    #1979      +/-   ##
==========================================
+ Coverage   91.87%   91.92%   +0.04%     
==========================================
  Files          27       27              
  Lines        2697     2713      +16     
  Branches      704      708       +4     
==========================================
+ Hits         2478     2494      +16     
  Misses        145      145              
  Partials       74       74              

Flag	Coverage Δ
integration	72.87% <100.00%> (+0.16%)	⬆️
unit	82.89% <18.75%> (-0.39%)	⬇️

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[oruebel]

2. For testing this, the ros3 test have some files that I think I could use, is that OK?

Yes, that should be fine

1. What streaming method should be used when an s3 path is passed

I think we should probably use fsspec as the default https://pynwb.readthedocs.io/en/latest/tutorials/advanced_io/streaming.html#streaming-method-1-fsspec

If installed, we could also use remfile https://pynwb.readthedocs.io/en/latest/tutorials/advanced_io/streaming.html#method-3-remfile and use fsspec as the fall-back. remfile tends to be a bit faster than fsspec, but I think fsspec is more widely used.

@bendichter what would you suggest for this?

[oruebel]

Aside from adding s3 and testing, the outline you started here looks good to me.

[h-mayorquin]

OK, I added s3 testing.

[h-mayorquin]

Is the test failing a permission issue?

[rly]

Seems like it was a codecov issue with detecting forks, perhaps when commits happen in quick succession: codecov/codecov-action#1580 . I re-ran the failing runs.

[oruebel]

Aside from the codecov question, this looks good to me. I approve the PR, because I assume the codecov question can probably be resolved in the comment, rather than requiring additional code changes, and it seems easier for me to re-approve if there are changes, rather than holding up the PR.