fix some testing issues

Author: lorenzocerrone

src/ngio/common/_pyramid.py

@@ -262,15 +262,10 @@ def init_empty_pyramid(
             **array_static_kwargs,
         )
 
-        _shape = [
+        ref_shape = [
             math.floor(s / sc) for s, sc in zip(ref_shape, scaling_factors, strict=True)
         ]
-        ref_shape = _shape
-
-        if chunks == "auto":
-            # We keep the same chunks as the first level
-            chunks = new_arr.chunks
-        else:
-            # Adjust chunks to not be larger than the new shape
-            chunks = tuple(min(c, s) for c, s in zip(chunks, ref_shape, strict=True))
+        chunks = tuple(
+            min(c, s) for c, s in zip(new_arr.chunks, ref_shape, strict=True)
+        )
     return None

src/ngio/images/_image.py

@@ -794,7 +794,7 @@ def derive_image_container(
         dimension_separator = find_dimension_separator(ref_image.zarr_array)
 
     if compressors is None:
-        compressors = ref_image.zaxxr_array.compressors  # type: ignore
+        compressors = ref_image.zarr_array.compressors  # type: ignore
 
     handler = create_empty_image_container(
         store=store,

src/ngio/utils/_zarr_utils.py

@@ -8,7 +8,7 @@
 from filelock import BaseFileLock, FileLock
 from zarr.abc.store import Store
 from zarr.core.array import CompressorLike
-from zarr.errors import ContainsGroupError, GroupNotFoundError
+from zarr.errors import ContainsGroupError
 from zarr.storage import FsspecStore, LocalStore, MemoryStore
 
 from ngio.utils import NgioFileExistsError, NgioFileNotFoundError, NgioValueError
@@ -38,13 +38,12 @@ def _check_store(store) -> NgioSupportedStore:
 
 def _check_group(group: zarr.Group, mode: AccessModeLiteral) -> zarr.Group:
     """Check the group and return a valid group."""
-    is_read_only = getattr(group, "_read_only", False)
-    if is_read_only and mode in ["w", "w-"]:
+    if group.read_only and mode in ["w", "w-"]:
         raise NgioValueError(
             "The group is read only. Cannot open in write mode ['w', 'w-']"
         )
 
-    if mode == "r" and not is_read_only:
+    if mode == "r" and not group.read_only:
         # let's make sure we don't accidentally write to the group
         group = zarr.open_group(store=group.store, path=group.path, mode="r")
 
@@ -75,14 +74,19 @@ def open_group_wrapper(
         _check_store(store)
         group = zarr.open_group(store=store, mode=mode, zarr_format=zarr_format)
 
-    except ContainsGroupError as e:
+    except FileExistsError as e:
         raise NgioFileExistsError(
             f"A Zarr group already exists at {store}, consider setting overwrite=True."
         ) from e
 
-    except GroupNotFoundError as e:
+    except FileNotFoundError as e:
         raise NgioFileNotFoundError(f"No Zarr group found at {store}") from e
 
+    except ContainsGroupError as e:
+        raise NgioFileExistsError(
+            f"A Zarr group already exists at {store}, consider setting overwrite=True."
+        ) from e
+
     return group
 
 
@@ -215,6 +219,19 @@ def remove_lock(self) -> None:
     @property
     def group(self) -> zarr.Group:
         """Return the group."""
+        if self._parallel_safe:
+            # If we are parallel safe, we need to reopen the group
+            # to make sure that the attributes are up to date
+            if self.mode == "r":
+                mode = "r"
+            else:
+                mode = "r+"
+            return zarr.open_group(
+                store=self._group.store,
+                path=self._group.path,
+                mode=mode,
+                zarr_format=self._group.metadata.zarr_format,
+            )
         return self._group
 
     def add_to_cache(self, key: str, value: object) -> None:
@@ -246,8 +263,7 @@ def load_attrs(self) -> dict:
 
     def _write_attrs(self, attrs: dict, overwrite: bool = False) -> None:
         """Write the metadata to the store."""
-        is_read_only = getattr(self._group, "_read_only", False)
-        if is_read_only:
+        if self.group.read_only:
             raise NgioValueError("The group is read only. Cannot write metadata.")
 
         # we need to invalidate the current attrs cache

tests/unit/common/test_pyramid.py

@@ -22,9 +22,9 @@ def test_on_disk_zooms(
     tmp_path: Path, order: InterpolationOrder, mode: Literal["dask", "numpy", "coarsen"]
 ):
     source = tmp_path / "source.zarr"
-    source_array = zarr.open_array(source, shape=(16, 128, 128), dtype="uint8")
+    source_array = zarr.create_array(source, shape=(16, 128, 128), dtype="uint8")
 
     target = tmp_path / "target.zarr"
-    target_array = zarr.open_array(target, shape=(16, 64, 64), dtype="uint8")
+    target_array = zarr.create_array(target, shape=(16, 64, 64), dtype="uint8")
 
     on_disk_zoom(source_array, target_array, order=order, mode=mode)

tests/unit/tables/test_backends.py

@@ -155,7 +155,7 @@ def test_parquet_backend(tmp_path: Path):
 
 def test_anndata_backend(tmp_path: Path):
     store = tmp_path / "test_anndata_backend.zarr"
-    handler = ZarrGroupHandler(store=store, cache=True, mode="a")
+    handler = ZarrGroupHandler(store=store, cache=True, mode="a", zarr_format=2)
     backend = AnnDataBackend()
     backend.set_group_handler(handler, index_type="int")
 

tests/unit/utils/test_zarr_utils.py

@@ -7,6 +7,7 @@
 import numpy as np
 import pytest
 import zarr
+from zarr.storage import LocalStore
 
 from ngio.utils import (
     NgioFileExistsError,
@@ -23,8 +24,8 @@ def test_group_handler_creation(tmp_path: Path, cache: bool):
     handler = ZarrGroupHandler(store=store, cache=cache, mode="a")
 
     _store = handler.group.store
-    assert isinstance(_store, zarr.DirectoryStore)
-    assert Path(_store.path) == store
+    assert isinstance(_store, LocalStore)
+    assert Path(_store.root.as_posix()) == store
     assert handler.use_cache == cache
 
     attrs = handler.load_attrs()
@@ -65,12 +66,12 @@ def test_group_handler_from_group(tmp_path: Path):
 def test_group_handler_read(tmp_path: Path):
     store = tmp_path / "test_group_handler_read.zarr"
 
-    group = zarr.group(store=store, overwrite=True)
+    group = zarr.create_group(store=store, overwrite=True)
     input_attrs = {"a": 1, "b": 2, "c": 3}
     group.attrs.update(input_attrs)
 
     group.create_group("group1")
-    group.create_dataset("array1", shape=(10, 10), dtype="int32")
+    group.create_array("array1", shape=(10, 10), dtype="int32")
 
     handler = ZarrGroupHandler(store=store, cache=True, mode="r")
 
@@ -97,10 +98,10 @@ def test_group_handler_read(tmp_path: Path):
 
 def test_open_fail(tmp_path: Path):
     store = tmp_path / "test_open_fail.zarr"
-    group = zarr.group(store=store, overwrite=True)
+    group = zarr.create_group(store=store, overwrite=True)
 
     read_only_group = open_group_wrapper(store=group, mode="r")
-    assert read_only_group._read_only
+    assert read_only_group.read_only
 
     with pytest.raises(NgioFileExistsError):
         open_group_wrapper(store=store, mode="w-")