[python] Include tiledbsoma_upgrade_shape for DenseNDArray

[johnkerl]

Issue and/or context: As tracked on issue #2407 / [sc-51048].

Note that the intended Python and R API changes are all agreed on and finalized as described in #2407.

Changes:

This was an omission on the 2.27 work.

Notes for Reviewer:

PR stacking as of today:

• main
• [python] Include tiledbsoma_upgrade_shape for DenseNDArray #3288
• [python] Run upgrade-shapes on notebook example experiments #3289
• Branch kerl/dataframe-shape-temp which is a copy of of Expose shape accessor for DataFrame [RFC] #3276, inserted here as a simplifying prerequisite as noted above
• [python] Re-run, and update, example notebooks with new shape feature #3290

[codecov]

Codecov Report

Attention: Patch coverage is 25.00000% with 12 lines in your changes missing coverage. Please review.

Project coverage is 83.61%. Comparing base (5f154bf) to head (86752ec).
Report is 7 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3288      +/-   ##
==========================================
- Coverage   83.67%   83.61%   -0.07%     
==========================================
  Files          51       51              
  Lines        5556     5571      +15     
==========================================
+ Hits         4649     4658       +9     
- Misses        907      913       +6     

Flag	Coverage Δ
python	83.61% <25.00%> (-0.07%)	⬇️

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

Components	Coverage Δ
python_api	83.61% <25.00%> (-0.07%)	⬇️
libtiledbsoma	∅ <ø> (∅)

[johnkerl]

Thanks @jp-dark !