Zarr 3.0 compatibility

requirements/requirements.txt

@@ -36,4 +36,4 @@ torchvision>=0.15.0
 tqdm>=4.64.1
 umap-learn>=0.5.3
 wsidicom>=0.18.0
-zarr>=2.13.3, <3.0.0
+zarr>=2.13.3

tiatoolbox/wsicore/wsireader.py

@@ -144,9 +144,9 @@ def is_ngff(  # noqa: PLR0911
     store = zarr.SQLiteStore(str(path)) if path.is_file() and is_sqlite3(path) else path
     try:
         zarr_group = zarr.open(store, mode="r")
-    except (zarr.errors.FSPathExistNotDir, zarr.errors.PathNotFoundError):
+    except Exception:  # skipcq: PYL-W0703  # noqa: BLE001
         return False
-    if not isinstance(zarr_group, zarr.hierarchy.Group):
+    if not isinstance(zarr_group, zarr.Group):
         return False
     group_attrs = zarr_group.attrs.asdict()
     try:
@@ -3527,8 +3527,9 @@ def page_area(page: tifffile.TiffPage) -> float:
         )
         self._zarr_lru_cache = zarr.LRUStoreCache(self._zarr_store, max_size=cache_size)
         self._zarr_group = zarr.open(self._zarr_lru_cache)
-        if not isinstance(self._zarr_group, zarr.hierarchy.Group):  # pragma: no cover
-            group = zarr.hierarchy.group()
+
+        if not isinstance(self._zarr_group, zarr.Group):
+            group = zarr.open_group()
             group[0] = self._zarr_group
             self._zarr_group = group
         self.level_arrays = {
@@ -5081,7 +5082,7 @@ def __init__(self: NGFFWSIReader, path: str | Path, **kwargs: dict) -> None:
 
         numcodecs.register_codecs()
         store = zarr.SQLiteStore(path) if is_sqlite3(path) else path
-        self._zarr_group: zarr.hierarchy.Group = zarr.open(store, mode="r")
+        self._zarr_group: zarr.Group = zarr.open(store, mode="r")
         attrs = self._zarr_group.attrs
         multiscales = attrs["multiscales"][0]
         axes = multiscales["axes"]