fixed the right value to be passed for chunk-shape in zarr 3

apps/hiopy/configure/configure.py

@@ -75,18 +75,20 @@ def add_variable(
 
         if zaxis is None:
             shape = (*ntime, crs_len)
-            _chunk_shape = (np.min(chunk_shape, shape),) if chunk_shape is not None else None
             _attributes["_ARRAY_DIMENSIONS"] = (*taxis_tuple, spatial_attr)
         else:
             nheight = g.get(zaxis).shape[0]
             shape = (*ntime, nheight, crs_len)
-            _chunk_shape = (np.min(chunk_shape, shape),) if chunk_shape is not None else None
             _attributes["_ARRAY_DIMENSIONS"] = (*taxis_tuple, zaxis, spatial_attr)
-        _attributes["grid_mapping"] = "crs"
 
+        _attributes["grid_mapping"] = "crs"
+        _chunk_shape = "auto"
         _shard_shape = None
-        if chunks_per_shard is not None:
-            _shard_shape = tuple(i * chunks_per_shard for i in _chunk_shape)
+
+        if chunk_shape is not None:
+            _chunk_shape = (np.min(chunk_shape, shape),)
+            if chunks_per_shard is not None:
+                _shard_shape = tuple(i * chunks_per_shard for i in _chunk_shape)
 
         v = g.create_array(
             name,

apps/hiopy/configure/create_dataset.py

@@ -5,7 +5,7 @@ import zarr
 
 
 def add_coordinates(
-    dataset: zarr.Dataset,
+    dataset: zarr.Group,
     coordinates: list[tuple[float, float]],
     coord_names: tuple[str, str] = ("lon", "lat"),
 ) -> None:
@@ -14,8 +14,8 @@ def add_coordinates(
 
     Parameters
     ----------
-    dataset : zarr.Dataset
-        The Zarr dataset where the coordinates will be added.
+    dataset : zarr.Group
+        The Zarr group where the coordinates will be added.
     coordinates : list[tuple[float, float]]
         A list of tuples containing the (longitude, latitude) values for each point.
     coord_names : tuple[str, str], optional
@@ -35,33 +35,31 @@ def add_coordinates(
 
     lat_list, lon_list = zip(*coordinates)
 
-    lon = dataset.create_array(
-        name=coord_names[0], fill_value=None, shape=lon_list.shape, dtype=np.float32
+    lon = dataset.create_dataset(
+        name=coord_names[0], data=np.array(lon_list), shape=(len(coordinates),)
     )
-    lon[:] = np.array(lon_list)
     lon.attrs["_ARRAY_DIMENSIONS"] = [coord_names[0]]
     lon.attrs["long_name"] = "longitude"
     lon.attrs["units"] = "degree"
     lon.attrs["standard_name"] = "grid_longitude"
 
-    lat = dataset.create_array(
-        name=coord_names[1], fill_value=None, shape=lat_list.shape, dtype=np.float32
+    lat = dataset.create_dataset(
+        name=coord_names[1], data=np.array(lat_list), shape=(len(coordinates),)
     )
-    lat[:] = np.array(lat_list)
     lat.attrs["_ARRAY_DIMENSIONS"] = [coord_names[1]]
     lat.attrs["long_name"] = "latitude"
     lat.attrs["units"] = "degree"
     lat.attrs["standard_name"] = "grid_latitude"
 
 
-def add_healpix_grid(dataset: zarr.Dataset, order: int):
+def add_healpix_grid(dataset: zarr.Group, order: int):
     """
         Add a HealPix grid to the specified Zarr dataset.
 
         Parameters
         ----------
-        dataset : zarr.Dataset
-            The Zarr dataset where the HealPix grid will be added to the crs.
+        dataset : zarr.Group
+            The Zarr group where the HealPix grid will be added to the crs.
         order : int
             The order of the HealPix grid. This corresponds to 2^order for the NSIDE.
 
@@ -78,7 +76,7 @@ def add_healpix_grid(dataset: zarr.Dataset, order: int):
 
 
 def add_healpix_hierarchy(
-    dataset: zarr.Dataset,
+    dataset: zarr.Group,
     order: int,
     nr_of_coarsenings: int = 4,
     prefix: str = "healpix_",
@@ -91,8 +89,8 @@ def add_healpix_hierarchy(
 
     Parameters
     ----------
-    dataset : zarr.Dataset
-        The Zarr dataset where the hierarchy will be added.
+    dataset : zarr.Group
+        The Zarr group where the hierarchy will be added.
     order : int
         The maximum level in the hierarchy.
     nr_of_coarsenings : int

requirements-dev.txt

@@ -5,4 +5,4 @@ pre-commit
 healpy
 zarr>=3
 aiohttp
-rich
\ No newline at end of file
+rich