[ci] Update github actions

[jp-dark]

Issue and/or context: Towards SOMA-892

Changes:

• Update the actions used for GitHub workflows.
• Fix missing shapely dependency that use to be indirectly included through somacore.

Note: The "TileDB-SOMA Docker build" failures are existing failures and will be addressed in a separate PR.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 85.42%. Comparing base (4c2aadc) to head (433c4f4).
⚠️ Report is 2 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #4434      +/-   ##
==========================================
- Coverage   85.42%   85.42%   -0.01%     
==========================================
  Files         136      136              
  Lines       21441    21441              
==========================================
- Hits        18317    18315       -2     
- Misses       3124     3126       +2     

Flag	Coverage Δ
python	88.35% <ø> (-0.03%)	⬇️
r	83.78% <ø> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

Components	Coverage Δ
python_api	88.35% <ø> (-0.03%)	⬇️
libtiledbsoma	∅ <ø> (∅)

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