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`sdata.write()` broken -> Reason why GH actions fail

Open timtreis opened this issue 2 years ago • 1 comments

MRE

from spatialdata.datasets import blobs

blobs().write("./blob.zarr")

fails with

FileNotFoundError: [Errno 2] No such file or directory: '/Users/tim.treis/Documents/GitHub/spatialdata-notebooks/notebooks/examples/blob.zarr/images/blobs_image/0/0/0/0'

Inspecting the created file shows that it only goes one 0 deep, so -> .../blobs_image/0/

timtreis avatar Sep 11 '23 14:09 timtreis

This seems like something I encountered here as well https://github.com/ome/ome-zarr-py/issues/304

The underlying issue is a change in the newest version of fsspec https://github.com/fsspec/filesystem_spec/commit/285094f0771dcc98467bf0a0e5e5b14a6cf096b3 that changed the way auto_mkdir works.

For the moment, a downgrade to fsspec<=2023.6.* should help in the short term until ome-zarr-py is fixed.

npeschke avatar Sep 11 '23 20:09 npeschke