zarr 2.18.7 incompatibility? "'int' object is not callable"

[hyanwong]

It appears as if compressed_array.nbytes_stored is an integer in zarr v2, not a function (which it is in zarr v3)

tszip.compress(ts_pq, "unified_genealogy/hgdp_tgp_sgdp_high_cov_ancients_chr9.tsz")
Traceback (most recent call last):
  File "<python-input-10>", line 1, in <module>
    tszip.compress(ts_pq, "unified_genealogy/hgdp_tgp_sgdp_high_cov_ancients_chr9.tsz")
    ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/well/kelleher/users/sbk774/conda/skylake/envs/adna/lib/python3.14/site-packages/tszip/compression.py", line 110, in compress
    compress_zarr(ts, root, variants_only=variants_only, chunk_size=chunk_size)
    ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/well/kelleher/users/sbk774/conda/skylake/envs/adna/lib/python3.14/site-packages/tszip/compression.py", line 269, in compress_zarr
    col.compress(root, compressor)
    ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^
  File "/well/kelleher/users/sbk774/conda/skylake/envs/adna/lib/python3.14/site-packages/tszip/compression.py", line 165, in compress
    nbytes_stored = compressed_array.nbytes_stored()
TypeError: 'int' object is not callable
>>> import zarr
>>> zarr.__version__
'2.18.7'
>>> tszip.__version__
'0.3.1'

[hyanwong]

Presumably we need to pin to zarr >= 3? That's a bit of a pain, as I want to use older versions of tsinfer with tszip, which only work with zarr < 3, but I can just install tszip 0.3.0 I guess.

[jeromekelleher]

Yes, we'll need to pin to zarr >= 3.x for the next release. Zarr 2.x is dead basically.

Weird this didn't show up before now though, as we should have been testing on Zarr v3 already. I suspect this snuck in on a recent point release of Zarr.

[jeromekelleher]

Ah, this is a zarr v2 compatibility issue, not Zarr v3. Hmm, looks like our v2/v3 tests weren't so good then. Ah well, we need to drop v2 anyway.