(feat): support for zarr-python>=3

[ilan-gold]

• Closes Support zarr v3 #1817
• Tests added
• Release note added (or unnecessary)

[codecov]

Codecov Report

Attention: Patch coverage is 90.32258% with 15 lines in your changes missing coverage. Please review.

Project coverage is 83.86%. Comparing base (3d0105b) to head (c10a99c).

Files with missing lines	Patch %	Lines
src/anndata/_io/specs/methods.py	93.75%	4 Missing ⚠️
src/anndata/_core/anndata.py	33.33%	2 Missing ⚠️
src/anndata/_io/zarr.py	81.81%	2 Missing ⚠️
src/anndata/_settings.py	80.00%	2 Missing ⚠️
src/anndata/compat/__init__.py	86.66%	2 Missing ⚠️
src/anndata/_io/h5ad.py	66.66%	1 Missing ⚠️
src/anndata/experimental/merge.py	92.30%	1 Missing ⚠️
src/anndata/tests/helpers.py	93.33%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1726      +/-   ##
==========================================
- Coverage   86.13%   83.86%   -2.28%     
==========================================
  Files          41       41              
  Lines        6277     6359      +82     
==========================================
- Hits         5407     5333      -74     
- Misses        870     1026     +156     

Files with missing lines	Coverage Δ
src/anndata/_core/sparse_dataset.py	92.35% <100.00%> (+0.20%)	⬆️
src/anndata/_io/specs/registry.py	94.44% <100.00%> (-0.48%)	⬇️
src/anndata/_io/utils.py	76.33% <ø> (ø)
src/anndata/abc.py	100.00% <ø> (ø)
src/anndata/_io/h5ad.py	92.27% <66.66%> (-0.42%)	⬇️
src/anndata/experimental/merge.py	87.20% <92.30%> (-0.24%)	⬇️
src/anndata/tests/helpers.py	82.49% <93.33%> (-10.73%)	⬇️
src/anndata/_core/anndata.py	81.44% <33.33%> (-0.20%)	⬇️
src/anndata/_io/zarr.py	82.55% <81.81%> (-0.99%)	⬇️
src/anndata/_settings.py	94.33% <80.00%> (+0.22%)	⬆️
... and 2 more

... and 4 files with indirect coverage changes

[ilan-gold]

blockers:

• v2 Object Encoding in 3.x.x python package zarr-developers/zarr-python#2500
• structured array encoding [v3] Structured dtype support zarr-developers/zarr-python#2134
• [v3] zarr.array from from an existing zarr.Array zarr-developers/zarr-python#2410

borderline blocker, TBD:

• Different Objects Pointing at the Same store_path can have different metadata zarr-developers/zarr-python#2716

non-blockers, but would be nice to fix:

• Inconsistent () indexing/size behavior from v2->v3 zarr-developers/zarr-python#2713
• keys/items yields two diferent results between v2 and v3 on ZipStore zarr-developers/zarr-python#2757

[flying-sheep]

why 3ac48cb? doesn’t the “minimum versions” job already check zarr v2?

[ilan-gold]

Ah yea, you're totally right.