First check for compatibility for zarr version 3 in storage backend

modelrunner/storage/backend/zarr.py

@@ -14,7 +14,18 @@
 import numpy as np
 import zarr
 from numpy.typing import ArrayLike, DTypeLike
-from zarr._storage.store import Store
+
+try:
+    # try import path from zarr version 3
+    from zarr.abc.store import Store
+
+    is_zarr2 = False
+
+except ImportError:
+    # try import path from zarr version 2
+    from zarr._storage.store import Store
+
+    is_zarr2 = True
 
 from ..access_modes import ModeType
 from ..attributes import AttrsLike
@@ -55,7 +66,10 @@
                 if self.mode.file_mode == "r":
                     self._logger.info("DirectoryStore is always opened writable")
 
-                self._store = zarr.DirectoryStore(path)
+                if is_zarr2:
+                    self._store = zarr.DirectoryStore(path)
+                else:
+                    self._store = zarr.LocalStore(path)
 
             elif path.suffix == ".zip":
                 # create a ZipStore
@@ -65,7 +79,7 @@
                     path.unlink()
                 self._store = zarr.storage.ZipStore(path, mode=file_mode)
 
-            elif path.suffix == ".sqldb":
+            elif is_zarr2 and path.suffix == ".sqldb":
                 # create a SQLiteStore
                 if self.mode.file_mode == "w" and path.exists():
                     self._logger.info("Delete file `%s`", path)
@@ -135,7 +149,7 @@
             return self._root.keys()  # type: ignore
 
     def is_group(self, loc: Sequence[str], *, ignore_cls: bool = False) -> bool:
-        return isinstance(self[loc], zarr.hierarchy.Group)
+        return isinstance(self[loc], zarr.Group)
 
     def _create_group(self, loc: Sequence[str]) -> None:
         parent, name = self._get_parent(loc)

pyproject.toml

@@ -37,7 +37,7 @@ all = [
     "h5py>=3.5",
     "pandas>=1.3",
     "PyYAML>=5",
-    "zarr>=2,<3",
+    "zarr>=2,<4",
 ]
 test = [
     "black>=19",

requirements_full.txt

@@ -1,4 +1,4 @@
 -r requirements.txt
 h5py>=3.5
 pandas>=1.3
-zarr>=2,<3
+zarr>=2,<4

tests/helpers/storage.py

@@ -42,7 +42,7 @@ def storage_extensions(
         dot (bool):
             Indicates whether the returned extensions are prepended with a dot (`.`)
         exclude (list, optional):
-            Extensions (without dots) that should be explicitely excluded
+            Extensions (without dots) that should be explicitly excluded
 
     Returns:
         sequence: sorted list of extensions
@@ -53,10 +53,12 @@ def storage_extensions(
     if module_available("h5py"):
         exts.append("hdf")
     if module_available("zarr"):
+        from modelrunner.storage.backend.zarr import is_zarr2
+
         exts.append("zip")
         if incl_folder:
             exts.extend(["", "zarr"])
-        if module_available("sqlite3"):
+        if is_zarr2 and module_available("sqlite3"):
             exts.append("sqldb")
 
     if dot: