(fix): correct typing of AnnData.X

[ilan-gold]

• Re: (chore): export read_elem and write_elem from the main package #1598 (comment)
• Tests added
• Release note added (or unnecessary)

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 84.32%. Comparing base (8f3299b) to head (1322408).
Report is 70 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1616      +/-   ##
==========================================
- Coverage   86.85%   84.32%   -2.53%     
==========================================
  Files          37       37              
  Lines        6027     6005      -22     
==========================================
- Hits         5235     5064     -171     
- Misses        792      941     +149     

Files with missing lines	Coverage Δ
src/anndata/_core/anndata.py	83.72% <100.00%> (ø)
src/anndata/_core/merge.py	83.91% <ø> (-11.08%)	⬇️
src/anndata/_core/storage.py	100.00% <100.00%> (ø)
src/anndata/_types.py	87.50% <100.00%> (-0.60%)	⬇️

... and 7 files with indirect coverage changes

[flying-sheep]

Shouldn’t we unify this with ArrayDataStructureType?

I don’t quite know why that one is an enum, maybe we can replace it with

ArrayDataStructureType = Union[All|Of|This|Here]

and then do

from typing import get_args

isinstance(get_args(ArrayDataStructureType))

[ilan-gold]

I don’t quite know why that one is an enum, maybe we can replace it with

I also didn't know but don't really question these sorts of things. I imagine it served a purpose at some point, but like I said in the related PR, that seems to have changed recently.

[flying-sheep]

I guess then we should unify the two. Either as part of this PR or later, as you wish

[flying-sheep]

We could maybe use __instancecheck__ and is_array_api_obj:

import array_api_compat

class ArrayApiMeta(type):
    def __instancecheck__(cls, instance: object) -> bool:
        return array_api_compat.is_array_api_obj(instance)

class ArrayApi(meta=ArrayApiMeta):
    pass

[ilan-gold]

I'm going to push back on the array-api here because I think it's out of scope and testing for it will be non-trivial. I think we should make a separate branch/PR for that specifically, and stick it in 0.12. We can test for jax, which now has a working CPU implementation (like numpy). This would be a very cool feature.

[ilan-gold]

There's even an issue for this: #1195. I will milestone/sprint it so we have it on the radar now.