fix: Made Patchly Zarr 3 compatible

Author: Karol-G

patchly/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.0.18"
+__version__ = "0.0.19"
 
 from patchly.sampler import GridSampler, SamplingMode
 from patchly.aggregator import Aggregator

patchly/aggregator.py

@@ -13,8 +13,10 @@
 
 try:
     import zarr
+    TYPE_ZARR_ARRAY = zarr.core.Array if hasattr(zarr.core, "Array") else zarr.core.array.Array
 except:
     zarr = None
+    TYPE_ZARR_ARRAY = None
 
 
 class PatchStatus(Enum):
@@ -427,7 +429,7 @@ def append(self, patch_h: npt.ArrayLike, patch_bbox_s: Union[Tuple, npt.ArrayLik
             for chunk_id in self.patch_chunk_dict[str(np.asarray(patch_bbox_s))]["chunks"]:
                 self.chunk_patch_dict[chunk_id][str(np.asarray(patch_bbox_s))]["status"] = PatchStatus.FILLED
                 if self.is_chunk_complete(chunk_id):
-                    if zarr is not None and isinstance(self.output_h.data, zarr.core.Array):
+                    if zarr is not None and isinstance(self.output_h.data, TYPE_ZARR_ARRAY):
                         warnings.warn("Ouput is a Zarr array. Switching to single threading for chunk processing. See issue #39 for more information.") # If issue is solved remove zarr and warnings import statements
                         self.process_chunk(chunk_id)
                     else:

patchly/array_like.py

@@ -9,14 +9,16 @@
 
 try:
     import zarr
+    TYPE_ZARR_ARRAY = zarr.core.Array if hasattr(zarr.core, "Array") else zarr.core.array.Array
 except:
     zarr = None
+    TYPE_ZARR_ARRAY = None
 
 
 def create_array_like(array_type, data, device=None):
     if array_type == np.ndarray or array_type is None:
         return NumpyArray(data, device)
-    elif zarr is not None and array_type == zarr.core.Array:
+    elif zarr is not None and array_type == TYPE_ZARR_ARRAY:
         return NumpyArray(data, device)
     elif torch is not None and array_type == torch.Tensor:
         if data is not None: