Work around various issues with Python 3.12

[johnkerl]

TL;DR we are trying to support Python 3.12 in TileDB-SOMA

Solved challenge:

As tracked from parent issue single-cell-data/TileDB-SOMA#1849

• [python] Try 3.12 again [WIP] TileDB-SOMA#2692
• [python] Work around pyarrow>=13 issue on MacOS, main branch TileDB-SOMA#2734
• Build the AWS SDK with hidden symbols. TileDB-Inc/TileDB#5223 went into core 2.26
• Now it's possible to put up PR [python] Python 3.12 support TileDB-SOMA#3001, and hope to release that in TileDB-SOMA 1.14 (TileDB-SOMA 1.14 TileDB-SOMA#2999)

Current unsolved challenges:

• Latest Python 3.12 is 3.12.5
  • As debug I tried Python 3.12.3 which worked as debug, but isn't a good option for shipping
• TileDB-SOMA's current typeguard version is 4.2.0
• Python 3.12.4 added a new required argument to evaluate_forward_ref within Python's built-in typing module which broke many packages including typeguard
• As a result, our TileDB-SOMA CI for PR 3001 fails like this
  • TypeError: ForwardRef._evaluate() missing 1 required keyword-only argument: 'recursive_guard'
• typeguard 4.3.0 contains a fix for this problem
  • https://github.com/agronholm/typeguard/releases
• But this surfaces another problem which is:

E       typeguard.TypeCheckError: item 0 of argument "coords" (tuple) did not match any element in the union:
E         NoneType: is not an instance of NoneType
E         int: is not an instance of int
E         somacore.types.Slice[int]: is not compatible with the Slice protocol because it has no attribute named '__orig_bases__'

/home/ubuntu/.pyenv/versions/3.12.5/lib/python3.12/site-packages/typeguard/_checkers.py:433: TypeCheckError

The current PR is an attempt to deal with this.

Once this works, we'll need to:

• Merge this PR
• Tag a release of this repo (somacore)
• Depend on 1.0.next of somacore within the TileDB-SOMA repo

I've currently got the following setup on an EC2 instance:

• somacore locally with pip install -e with this PR checked out
• tiledbsoma locally with pip install -e with [python] Python 3.12 support TileDB-SOMA#3001 checked out

[thetorpedodog]

If this is necessary that’s fine, I guess, but this should already be covered under ValSliceOrSequence[int], since that includes a Sequence[int], which is a supertype of Tuple[int, ...].

[thetorpedodog]

This is a typeguard bug—it’s checking too many built-in attributes of the protocol that don’t actually matter. (See, for example, a case where it rejects objects with a completely empty protocol that I found.

That said, if implementing this makes typeguard stop complaining for now, I would do two things:

1. Add a comment to that effect, and that it should be removed at some point
2. Make this function instead raise AssertionError, since it should never be called.

[ryan-williams]

I believe this PR is no longer necessary; tests+lint have passed on 3.12 in this repo since #186, and single-cell-data/TileDB-SOMA#3001 has 3.12 passing without requiring any somacore changes.

[johnkerl]

Awesome, thanks @ryan-williams !