Remove references to hdmf.Array and region references

[rly]

Motivation

Address hdmf.Array deprecation. Fix #235

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-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 86.36%. Comparing base (b69c3e0) to head (f423f41).

Additional details and impacted files

@@            Coverage Diff             @@
##              dev     #236      +/-   ##
==========================================
+ Coverage   85.58%   86.36%   +0.77%     
==========================================
  Files           5        5              
  Lines        1214     1188      -26     
  Branches      304      297       -7     
==========================================
- Hits         1039     1026      -13     
+ Misses        113      103      -10     
+ Partials       62       59       -3     

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