Fix errors caused by zarr

Author: constantinpape

environment.yaml

@@ -13,4 +13,5 @@ dependencies:
   - s3fs
   - torch_em
   - z5py
-  - zarr
+  # Don't install zarr v3, as we are not sure that it is compatible with MoBIE etc. yet
+  - zarr <3

flamingo_tools/file_utils.py

@@ -7,6 +7,11 @@
 import zarr
 from elf.io import open_file
 
+try:
+    from zarr.abc.store import Store
+except ImportError:
+    from zarr._storage.store import BaseStore as Store
+
 
 def _parse_shape(metadata_file):
     depth, height, width = None, None, None
@@ -62,7 +67,7 @@ def read_tif(file_path: str) -> Union[np.ndarray, np.memmap]:
     return x
 
 
-def read_image_data(input_path: Union[str, zarr.storage.FSStore], input_key: Optional[str]) -> np.typing.ArrayLike:
+def read_image_data(input_path: Union[str, Store], input_key: Optional[str]) -> np.typing.ArrayLike:
     """Read flamingo image data, stored in various formats.
 
     Args:

flamingo_tools/s3_utils.py

@@ -7,6 +7,11 @@
 import s3fs
 import zarr
 
+try:
+    from zarr.abc.store import Store
+except ImportError:
+    from zarr._storage.store import BaseStore as Store
+
 
 # Dedicated bucket for cochlea lightsheet project
 MOBIE_FOLDER = "/mnt/vast-nhr/projects/nim00007/data/moser/cochlea-lightsheet/mobie_project/cochlea-lightsheet"
@@ -93,7 +98,7 @@ def get_s3_path(
     bucket_name: Optional[str] = None,
     service_endpoint: Optional[str] = None,
     credential_file: Optional[str] = None,
-) -> Tuple[zarr.storage.FSStore, s3fs.core.S3FileSystem]:
+) -> Tuple[Store, s3fs.core.S3FileSystem]:
     """Get S3 path for a file or folder and file system based on S3 parameters and credentials.
 
     Args: