Small adjustments to the spatial branch

[jp-dark]

• Rename [obs|var]_scene -> [obs|var]_spatial_presence
• Default to not creating var_spatial_presence dataframe when ingesting cellxgene hdf5 files
• Fix the obsl[loc] dataframe to only have columns for the soma_joinid and location data (position & spot size)

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 0% with 12 lines in your changes missing coverage. Please review.

Project coverage is 85.10%. Comparing base (e53daad) to head (4f5272b). Report is 1 commits behind head on spatial.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## spatial #2907 +/- ## =========================================== + Coverage 84.96% 85.10% +0.13% =========================================== Files 42 42 Lines 4356 4356 =========================================== + Hits 3701 3707 +6 + Misses 655 649 -6 ``` | [Flag](https://app.codecov.io/gh/single-cell-data/TileDB-SOMA/pull/2907/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data) | Coverage Δ | | |---|---|---| | [python](https://app.codecov.io/gh/single-cell-data/TileDB-SOMA/pull/2907/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data) | `85.10% <0.00%> (+0.13%)` | :arrow_up: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data#carryforward-flags-in-the-pull-request-comment) to find out more. | [Components](https://app.codecov.io/gh/single-cell-data/TileDB-SOMA/pull/2907/components?src=pr&el=components&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data) | Coverage Δ | | |---|---|---| | [python_api](https://app.codecov.io/gh/single-cell-data/TileDB-SOMA/pull/2907/components?src=pr&el=component&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data) | `85.10% <0.00%> (+0.13%)` | :arrow_up: | | [libtiledbsoma](https://app.codecov.io/gh/single-cell-data/TileDB-SOMA/pull/2907/components?src=pr&el=component&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data) | `∅ <ø> (∅)` | |