[python] Re-introduce tiledb_ctx for SOMATileDBContext

[nguyenv]

Issue and/or context:

[sc-58711]

Changes:

• Re-introduce the tiledb_ctx argument
• Correct documentation
• Update typing

Notes for Reviewer:

We are not reintroducing tiledb-py as a dependency. The tiledb_ctx is only usable when tiledb-py is installed.

[codecov]

Codecov Report

Attention: Patch coverage is 80.85106% with 9 lines in your changes missing coverage. Please review.

Project coverage is 85.89%. Comparing base (d1178ae) to head (7cc7245).
Report is 18 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3335      +/-   ##
==========================================
+ Coverage   85.87%   85.89%   +0.02%     
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  Files          55       55              
  Lines        6143     6176      +33     
==========================================
+ Hits         5275     5305      +30     
- Misses        868      871       +3     

Flag	Coverage Δ
python	85.89% <80.85%> (+0.02%)	⬆️

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Components	Coverage Δ
python_api	85.89% <80.85%> (+0.02%)	⬆️
libtiledbsoma	∅ <ø> (∅)

[bkmartinjr]

Couple of issues:

1. The PR is missing the tiledb_ctx property that was present in the API. This is the first point mentioned in the bug report. Previously it was possible to do the following:

context = soma.SOMATileDBContext()
A = tiledb.open(uri, ctx=context.tiledb_ctx)

We did deprecate this property in 1.14.5, so removing it is fair game. I'm just unsure what decision @aaronwolen took - the bug report suggests that he wanted to add both back, but I may be misreading it.

Recommend checking with him to confirm removal.

2. There are some minor style/pattern comments inline.

[teo-tsirpanis]

Suggested change

	tiledb_config: Dict[str, Union[str, float]] | None = None,
	tiledb_ctx: "tiledb.Ctx" | None = None,
	tiledb_config: Dict[str, Union[str, float]] | "tiledb.Ctx" | None = None,

I would slightly prefer this. Admittedly passing a context to the tiledb_config doesn't sound very good, but it eliminates the error case of passing both a context and a config. You could take a leap and say that a context is part of the "configuration".

[nguyenv]

I did considering having tiledb_config also take in a tiledb.Ctx but decided to revert back to how we previously had it as separate arguments. But I'm open to further discussion about only having a tiledb_config argument now.

[bkmartinjr]

I don't think _tiledb_ctx is a method, so I suspect this should drop the parens, e.g.,

cfg = self._tiledb_ctx.config().dict()

[bkmartinjr]

ps. assuming my comment is correct, does this imply a missing test case? (or my comment is wrong!)

[nguyenv]

You are right that there should not be parens.

The missing test case brings up a another issue though. We have removed all tiledb-py usage from the unit tests. But should we temporarily re-introduce it for testing with tiledb.Ctx()? We would xskip the test if tiledb is not installed locally. But then do we need to install tiledb for CI runs? (cc @johnkerl)

[bkmartinjr]

yeah, tough one. I don't see any great solution - options?

The best I can come up with is:

1. Code the tests to work both with and without the package installed:
   • if installed, test that it works as expected
   • if not installed, test that it generates the right error
2. Have two CI's: one with it installed, one with it not installed

That at least mimics real-world conditions.

[bkmartinjr]

couple of minor suggestions/issues

[bkmartinjr]

Nice, this is much cleaner. TY @nguyenv