Zarr3

funlib/persistence/arrays/datasets.py

@@ -13,15 +13,6 @@
 
 logger = logging.getLogger(__name__)
 
-
-class ArrayNotFoundError(Exception):
-    """Exception raised when an array is not found in the dataset."""
-
-    def __init__(self, message: str = "Array not found in the dataset"):
-        self.message = message
-        super().__init__(self.message)
-
-
 def open_ds(
     store,
     mode: str = "r",
@@ -107,10 +98,7 @@ def open_ds(
         else get_default_metadata_format()
     )
 
-    try:
-        data = zarr.open(store, mode=mode, **kwargs)
-    except zarr.errors.PathNotFoundError:
-        raise ArrayNotFoundError(f"Nothing found at path {store}")
+    data = zarr.open(store, mode=mode, **kwargs)
 
     metadata = metadata_format.parse(
         data.shape,
@@ -239,7 +227,7 @@ def prepare_ds(
 
     try:
         existing_array = open_ds(store, mode="r", **kwargs)
-    except ArrayNotFoundError:
+    except FileNotFoundError:
         existing_array = None
 
     if existing_array is not None:
@@ -349,18 +337,14 @@ def prepare_ds(
     )
 
     # create the dataset
-    try:
-        ds = zarr.open_array(
-            store=store,
-            shape=shape,
-            chunks=chunk_shape,
-            dtype=dtype,
-            dimension_separator="/",
-            mode=mode,
-            **kwargs,
-        )
-    except zarr.errors.ArrayNotFoundError:
-        raise ArrayNotFoundError(f"Nothing found at path {store}")
+    ds = zarr.open_array(
+        store=store,
+        shape=shape,
+        chunks=chunk_shape,
+        dtype=dtype,
+        mode=mode,
+        **kwargs,
+    )
 
     default_metadata_format = get_default_metadata_format()
     our_metadata = {

funlib/persistence/arrays/metadata.py

@@ -305,7 +305,7 @@ def recurse(
             # base case
             if len(keys) == 0:
                 # this key returns the data we want
-                if isinstance(data, (dict, zarr.attrs.Attributes)):
+                if isinstance(data, (dict, zarr.core.attributes.Attributes)):
                     return data.get(str(current_key), None)
                 elif isinstance(data, list):
                     assert isinstance(current_key, int), current_key

pyproject.toml

@@ -13,12 +13,12 @@ authors = [
 ]
 dynamic = ['version']
 
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 classifiers = ["Programming Language :: Python :: 3"]
 keywords = []
 
 dependencies = [
-    "zarr>=2,<3",
+    "zarr>=3,<4",
     # ImportError: cannot import name 'cbuffer_sizes' from 'numcodecs.blosc'
     # We can pin zarr to >2.18.7 but then we have to drop python 3.10
     # pin numcodecs to avoid breaking change
@@ -63,3 +63,6 @@ explicit_package_bases = true
 [[tool.mypy.overrides]]
 module = ["zarr.*", "iohub.*"]
 ignore_missing_imports = true
+
+[tool.uv.sources]
+iohub = { git = "https://github.com/czbiohub-sf/iohub", rev = "zarr3-dev" }

tests/conftest.py

@@ -35,19 +35,17 @@ def can_connect_to_psql():
         psql_param,
     )
 )
-def provider_factory(request, tmpdir):
+def provider_factory(request, tmp_path):
     # provides a factory function to generate graph provider
     # can provide either mongodb graph provider or file graph provider
     # if file graph provider, will generate graph in a temporary directory
     # to avoid artifacts
 
-    tmpdir = Path(tmpdir)
-
     def sqlite_provider_factory(
         mode, directed=None, total_roi=None, node_attrs=None, edge_attrs=None
     ):
         return SQLiteGraphDataBase(
-            tmpdir / "test_sqlite_graph.db",
+            tmp_path / "test_sqlite_graph.db",
             position_attribute="position",
             mode=mode,
             directed=directed,

tests/test_datasets.py

@@ -2,7 +2,7 @@
 import pytest
 
 from funlib.geometry import Coordinate, Roi
-from funlib.persistence.arrays.datasets import ArrayNotFoundError, open_ds, prepare_ds
+from funlib.persistence.arrays.datasets import open_ds, prepare_ds
 from funlib.persistence.arrays.metadata import MetaDataFormat
 
 stores = {
@@ -16,8 +16,8 @@
 
 
 @pytest.mark.parametrize("store", stores.keys())
-def test_metadata(tmpdir, store):
-    store = tmpdir / store
+def test_metadata(tmp_path, store):
+    store = tmp_path / store
 
     # test prepare_ds creates array if it does not exist and mode is write
     array = prepare_ds(
@@ -34,10 +34,10 @@ def test_metadata(tmpdir, store):
 
 @pytest.mark.parametrize("store", stores.keys())
 @pytest.mark.parametrize("dtype", [np.float32, np.uint8, np.uint64])
-def test_helpers(tmpdir, store, dtype):
+def test_helpers(tmp_path, store, dtype):
     shape = Coordinate(1, 1, 10, 20, 30)
     chunk_shape = Coordinate(2, 3, 10, 10, 10)
-    store = tmpdir / store
+    store = tmp_path / store
     metadata = MetaDataFormat().parse(
         shape,
         {
@@ -50,7 +50,7 @@ def test_helpers(tmpdir, store, dtype):
     )
 
     # test prepare_ds fails if array does not exist and mode is read
-    with pytest.raises(ArrayNotFoundError):
+    with pytest.raises(FileNotFoundError):
         prepare_ds(
             store,
             shape,
@@ -218,9 +218,9 @@ def test_helpers(tmpdir, store, dtype):
 
 @pytest.mark.parametrize("store", stores.keys())
 @pytest.mark.parametrize("dtype", [np.float32, np.uint8, np.uint64])
-def test_open_ds(tmpdir, store, dtype):
+def test_open_ds(tmp_path, store, dtype):
     shape = Coordinate(1, 1, 10, 20, 30)
-    store = tmpdir / store
+    store = tmp_path / store
     metadata = MetaDataFormat().parse(
         shape,
         {
@@ -233,7 +233,7 @@ def test_open_ds(tmpdir, store, dtype):
     )
 
     # test open_ds fails if array does not exist and mode is read
-    with pytest.raises(ArrayNotFoundError):
+    with pytest.raises(FileNotFoundError):
         open_ds(
             store,
             offset=metadata.offset,

tests/test_metadata.py

@@ -91,15 +91,15 @@ def test_empty_metadata():
     assert metadata.types == ["space", "space", "space", "space", "space"]
 
 
-def test_default_metadata_format(tmpdir):
+def test_default_metadata_format(tmp_path):
     set_default_metadata_format(metadata_formats["simple"])
     metadata = metadata_formats["simple"].parse(
         (10, 2, 100, 100, 100),
         json.loads(open(fixtures_dir / metadata_jsons["simple"]).read()),
     )
 
     prepare_ds(
-        tmpdir / "test.zarr/test",
+        tmp_path / "test.zarr/test",
         (10, 2, 100, 100, 100),
         offset=metadata.offset,
         voxel_size=metadata.voxel_size,
@@ -110,7 +110,7 @@ def test_default_metadata_format(tmpdir):
         mode="w",
     )
 
-    zarr_attrs = dict(**zarr.open(str(tmpdir / "test.zarr/test")).attrs)
+    zarr_attrs = dict(**zarr.open(tmp_path / "test.zarr/test").attrs)
     assert zarr_attrs["offset"] == [100, 200, 400]
     assert zarr_attrs["resolution"] == [1, 2, 3]
     assert zarr_attrs["extras/axes"] == ["sample^", "channel^", "t", "y", "x"]