Tighten up warnings context management

[BrianMichell]

Resolves #864

Bumping zarr to 3.3.0 removes the warning for our normal structured headers. It does not remove the warning for raw headers.

Also took this chance to delete the numcodecs warning since this is no longer used.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.04%. Comparing base (c3ba558) to head (d5475a5).
⚠️ Report is 253 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #873      +/-   ##
==========================================
+ Coverage   85.30%   93.04%   +7.73%     
==========================================
  Files          46      147     +101     
  Lines        2219     8393    +6174     
  Branches      306      469     +163     
==========================================
+ Hits         1893     7809    +5916     
- Misses        281      510     +229     
- Partials       45       74      +29     

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