zarr version question

[vthorsson]

Hi Minerva team,
Thanks for making this tool available. I've been using the precompiled version of Minerva Author but for another reason I would like to see if I can get it going from source .

I've retrieved the minerva-author from github and followed the directions for setting up the right environment using requirements.yaml.
I get a package version error after selecting the image file with the app. See error trace below.
The version of the packages installed with the conda env comment provided is seen here

zarr                      2.18.7             pyhd8ed1ab_0    conda-forge
tifffile                  2025.6.11          pyhd8ed1ab_0    conda-forge

Any thoughts on how to deal with the error?

(I get the error on two different computers, am using MacOS 15.5 on both)

Thanks !

Vésteinn Thorsson
Institute for Systems Biology

python src/app.py
Running server with 10 threads
Opening file:  /Users/vthorsson/ST-Analytics/G4D3/G4D3_Slide5_020325_Scan1.ome.tiff
330
ERROR:root:zarr 2.18.7 < 3 is not supported
Traceback (most recent call last):
  File "/Users/vthorsson/opt/miniconda3/envs/minerva-author-new/lib/python3.13/site-packages/tifffile/zarr.py", line 49, in <module>
    from zarr.abc.store import ByteRequest, Store
ModuleNotFoundError: No module named 'zarr.abc'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/Users/vthorsson/ST-Analytics/minerva-author/src/app.py", line 1829, in api_import
    (invalid, opener) = return_image_opener(str(input_image_file))
                        ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/vthorsson/ST-Analytics/minerva-author/src/app.py", line 750, in return_image_opener
    opener = return_opener(path, "image_openers")
  File "/Users/vthorsson/ST-Analytics/minerva-author/src/app.py", line 665, in return_opener
    opener = Opener(path)
  File "/Users/vthorsson/ST-Analytics/minerva-author/src/app.py", line 292, in __init__
    self.group = zarr.open(self.io.series[0].aszarr())
                           ~~~~~~~~~~~~~~~~~~~~~~~~^^
  File "/Users/vthorsson/opt/miniconda3/envs/minerva-author-new/lib/python3.13/site-packages/tifffile/tifffile.py", line 12504, in aszarr
    from .zarr import ZarrTiffStore
  File "/Users/vthorsson/opt/miniconda3/envs/minerva-author-new/lib/python3.13/site-packages/tifffile/zarr.py", line 53, in <module>
    raise ValueError(f'zarr {zarr.__version__} < 3 is not supported') from exc
ValueError: zarr 2.18.7 < 3 is not supported

[vthorsson]

I dug into this a little more and it looks like tifffile version 2025.6.11 hits an error trying to execute
from zarr.abc.store import ByteRequest, Store in zarr.py

In requirements.yaml I changed

tifffile>=2025.5.10

to

tifffile=2025.5.10

and that appears to have resolved this. The problem was with the tifffile version, not the zarrr version.