Revise pyproject.toml and pre-commit hooks based on repo review

[rlskoeser]

The Scientific Python repo-review tool was included in the original technical design document, in the developer-facing notes, which I was reminded of when I revised it recently in #338 .

Ran the review and made the recommended changes that were easy (does not address all flagged items).

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 99.65%. Comparing base (3799c3c) to head (7f2fde0).
⚠️ Report is 1 commits behind head on develop.

Additional details and impacted files

@@           Coverage Diff            @@
##           develop     #339   +/-   ##
========================================
  Coverage    99.65%   99.65%           
========================================
  Files           32       32           
  Lines         2336     2336           
  Branches       101      101           
========================================
  Hits          2328     2328           
  Misses           1        1           
  Partials         7        7           

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