ExternalResources I/O

[mavaylon1]

Motivation

What was the reasoning behind this change? Please explain the changes briefly.

This is to add logic to support ExternalResources on HDMFIO and HDF5IO. This was set up due to pynwb (https://github.com/NeurodataWithoutBorders/pynwb/actions/runs/5488375497?pr=1684). The update simply sets up external resources in the corresponding init methods.

How to test the behavior?

Show how to reproduce the new behavior (can be a bug fix or a new feature)

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 ruff 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.

[codecov]

Codecov Report

Patch coverage: 94.73% and no project coverage change.

Comparison is base (0c01dd7) 88.23% compared to head (93a2c01) 88.24%.

Additional details and impacted files

@@           Coverage Diff           @@
##              dev     #895   +/-   ##
=======================================
  Coverage   88.23%   88.24%           
=======================================
  Files          45       45           
  Lines        9232     9247   +15     
  Branches     2638     2641    +3     
=======================================
+ Hits         8146     8160   +14     
  Misses        768      768           
- Partials      318      319    +1     

Impacted Files	Coverage Δ
src/hdmf/backends/io.py	96.10% <94.11%> (-0.68%)	⬇️
src/hdmf/backends/hdf5/h5tools.py	82.36% <100.00%> (ø)

☔ View full report in Codecov by Sentry.
📢 Do you have feedback about the report comment? Let us know in this issue.

[oruebel]

Overall, this looks good to me. I'm wondering whether this should also include the reading of the ExternalResources file in HDMFIO.read:

if self.external_resources is not None:
            er_read = ExternalResources.from_norm_tsv(path=self.external_resources)
            file.link_resources(er_read)

[mavaylon1]

Overall, this looks good to me. I'm wondering whether this should also include the reading of the ExternalResources file in HDMFIO.read:

if self.external_resources is not None:
            er_read = ExternalResources.from_norm_tsv(path=self.external_resources)
            file.link_resources(er_read)

I did the local import, but without the link_resources since that exists only on ExternalResourcesManager.

[mavaylon1]

I see there's a test missing. I'll add it.

[mavaylon1]

Given that py3.7 has made it to the special farm upstate, can we ignore the conda 3.7 test issue? @rly

We should also make the update to remove it on a new ticket.

[mavaylon1]

@oruebel could you give this a gander so we can do a release and then merge the pynwb PR.

[oruebel]

Looks good to me