Minor project updates

[stephprince]

Motivation

Minor updates to fix build errors in the run all tests GH action and to apply the upper bound to hdmf that was discussed in #2030 (comment)

These changes are intended to be merged into the release-3.0.0 branch.

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 check . && codespell 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

All modified and coverable lines are covered by tests ✅

Project coverage is 92.84%. Comparing base (9d7bad1) to head (abeeeec).
Report is 1 commits behind head on release-3.0.0.

Additional details and impacted files

@@              Coverage Diff               @@
##           release-3.0.0    #2040   +/-   ##
==============================================
  Coverage          92.84%   92.84%           
==============================================
  Files                 28       28           
  Lines               2755     2755           
  Branches             716      716           
==============================================
  Hits                2558     2558           
  Misses               127      127           
  Partials              70       70           

Flag	Coverage Δ
integration	73.72% <ø> (ø)
unit	82.75% <ø> (ø)

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[stephprince]

@rly I think readthedocs is flaky at the moment and I don't think the failing link check is related to this PR