import error with Zarr version 3.0.0

[kaczmarj]

hi all, zarr 3.0.0 was released several days ago, and there seems to be an incompatibility in tiffslide.

i installed tiffslide with the latest zarr and saw an ImportError: "cannot import name 'BaseStore' from 'zarr.storage'". installing zarr<3.0 fixed that error.

$ python -m pip install tiffslide

$ python -c 'import tiffslide'
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/private/tmp/fo/venv/lib/python3.12/site-packages/tiffslide/__init__.py", line 9, in <module>
    from tiffslide.tiffslide import PROPERTY_NAME_BACKGROUND_COLOR
  File "/private/tmp/fo/venv/lib/python3.12/site-packages/tiffslide/tiffslide.py", line 41, in <module>
    from tiffslide._zarr import get_zarr_depth_and_dtype
  File "/private/tmp/fo/venv/lib/python3.12/site-packages/tiffslide/_zarr.py", line 17, in <module>
    from zarr.storage import BaseStore
ImportError: cannot import name 'BaseStore' from 'zarr.storage' (/private/tmp/fo/venv/lib/python3.12/site-packages/zarr/storage/__init__.py)

[kaczmarj]

i'm not sure how to fix the code on the tiffslide part. there is zarr.abc.store.Store, which is an abstract base class. there is also zarr.storage.StoreLike.

[ap--]

Thanks for reporting!

We just pin zarr<3 and release a new version.

Moving to zarr 3 will require more refactoring.

Would you be willing to make the PR?

Cheers, Andreas 😊

[kaczmarj]

yes, i can do that

[ap--]

Seems like there are more issues now...

https://github.com/Bayer-Group/tiffslide/actions/runs/12770125583/job/35594233326

Needs some further investigation.

[kaczmarj]

here's a snippet of some of the errors:

FAILED tiffslide/tests/test_tiffslide.py::test_read_region_nopadding_oob[generated-pyramidal-1ch-16b-svs] - NotImplementedError: series with axes='ZYX' not supported yet
FAILED tiffslide/tests/test_tiffslide.py::test_padding_no_padding[generated-pyramidal-1ch-16b-svs] - NotImplementedError: series with axes='ZYX' not supported yet
FAILED tiffslide/tests/test_tiffslide.py::test_padding_br_on_nonzero_level[generated-pyramidal-1ch-16b-svs] - NotImplementedError: series with axes='ZYX' not supported yet
FAILED tiffslide/tests/test_tiffslide.py::test_no_numpy_scalar_overflow[generated-pyramidal-1ch-16b-svs] - NotImplementedError: series with axes='ZYX' not supported yet
FAILED tiffslide/tests/test_zarr.py::test_get_chunk_sizes[generated-pyramidal-1ch-16b-svs] - NotImplementedError: series with axes='ZYX' not supported yet
FAILED tiffslide/tests/test_zarr.py::test_decode_only_once[generated-pyramidal-1ch-16b-svs] - NotImplementedError: series with axes='ZYX' not supported yet

looks like the errors are all coming from https://github.com/Bayer-Group/tiffslide/blob/d1ef04a6fa1d7b528edaf78bdb684b9ed8263c51/tiffslide/tiffslide.py#L719

the tests are using zarr 2.18.4, so 3x isn't the issue.

[ap--]

Probably caused by some combination of kerchunk and/or/xor tifffile that need pinning too...

[kaczmarj]

i can reproduce the error on my local machine, with a fresh install of the main branch of tiffslide and a fresh pip install -e .[dev]. i tested different versions of tifffile, and the version v2024.8.24 is the earliest version that causes the error in tiffslide.

taking a look at the diffs between v2024.8.24 and the latest working version, v2024.8.10, there was a change regarding axes.

[kaczmarj]

changing this line fixes the tests that errored with the ZYX error:

- "metadata": None,
+ "metadata": {"axes": "YX"},

but then tifffile has the following complaints:

ERROR    tifffile:tifffile.py:4907 <tifffile.TiffFile '_small_pyramid_2.svs'> shaped series axes do not match shape
ERROR    tifffile:tifffile.py:4886 <tifffile.TiffFile '_small_pyramid_2.svs'> invalid shaped series metadata or corrupted file