[c++] Hide internal dimensions

[XanthosXanthopoulos]

Geometry dataframe creates some extra internal dimensions to support spatial indexing. When returning back the index column names and arrow schema these dimensions (being implementation-specific) should be hidden and replaces with soma_geometry as index column.

Additionally setting a range for spatial axes should only need the axis name and not the internal index names.

[jp-dark]

Looks like you can change the implementation so these are passed as const references instead of pointers without too much pain.

[johnkerl]

Please include in this PR's description some copy/paste of:

• Example use of how the user might keystroke out the index_column_names and domain at create
  • Either for SOMAGeometryDataFrame.create, and/or
  • For an ingestion step at the experiment level
• What domain might look like when they read it back

Also:

• Please file a follow-on PR to update https://github.com/single-cell-data/TileDB-SOMA/tree/main/apis/python/notebooks

[codecov]

Codecov Report

Attention: Patch coverage is 11.33333% with 133 lines in your changes missing coverage. Please review.

Project coverage is 66.83%. Comparing base (946d3f7) to head (87cef7c).

Additional details and impacted files

@@             Coverage Diff             @@
##             main    #3266       +/-   ##
===========================================
- Coverage   85.14%   66.83%   -18.32%     
===========================================
  Files          53      138       +85     
  Lines        5568    17689    +12121     
  Branches        0     1108     +1108     
===========================================
+ Hits         4741    11822     +7081     
- Misses        827     5484     +4657     
- Partials        0      383      +383     

Flag	Coverage Δ
libtiledbsoma	58.36% <11.33%> (?)
python	85.25% <ø> (+0.10%)	⬆️

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Components	Coverage Δ
python_api	85.25% <ø> (+0.10%)	⬆️
libtiledbsoma	53.17% <10.13%> (∅)

[johnkerl]

You reference both of these throughout

*this->ctx()->tiledb_ctx(), *this->tiledb_schema())

Please make an

auto ctx = this->ctx()->tiledb_ctx();

and

auto schema = this->tiledb_schema();

[johnkerl]

I wish you had made these helpers as a separate PR. As an ongoing ask I am continuing to ask for split-out PRs.

This PR is only 300 lines, which isn't a lot, but, all the codecov warnings are making this hard to read -- as if it had been a high-line-count PR.

[johnkerl]

I ask you to split this not due to high line count but because you've got two different things going on. Pulling out helper functions is distinct from the goal of the PR (hiding internal dimensions) and is worth a separate PR. Then you can stack the dimension-hiding on top of it as a second PR.

[johnkerl]

Specifically, please split out a PR with only the arrow_adapter.h and arrow_adapter.cc mods. That, I will understand quickly, and will be able to review quickly.