fix: opening a group with unspecified format finds either v2 or v3 (#2183)

metadata objects

Author: jhamman

src/zarr/api/asynchronous.py

@@ -9,6 +9,7 @@
 
 from zarr.core.array import Array, AsyncArray
 from zarr.core.common import JSON, AccessModeLiteral, ChunkCoords, MemoryOrder, ZarrFormat
+from zarr.core.config import config
 from zarr.core.group import AsyncGroup
 from zarr.core.metadata.v2 import ArrayV2Metadata
 from zarr.core.metadata.v3 import ArrayV3Metadata
@@ -126,8 +127,7 @@ def _handle_zarr_version_or_format(
 
 def _default_zarr_version() -> ZarrFormat:
     """return the default zarr_version"""
-    # TODO: set default value from config
-    return 3
+    return cast(ZarrFormat, int(config.get("default_zarr_version", 3)))
 
 
 async def consolidate_metadata(*args: Any, **kwargs: Any) -> AsyncGroup:
@@ -337,7 +337,10 @@ async def save_group(
     kwargs
         NumPy arrays with data to save.
     """
-    zarr_format = _handle_zarr_version_or_format(zarr_version=zarr_version, zarr_format=zarr_format)
+    zarr_format = (
+        _handle_zarr_version_or_format(zarr_version=zarr_version, zarr_format=zarr_format)
+        or _default_zarr_version()
+    )
 
     if len(args) == 0 and len(kwargs) == 0:
         raise ValueError("at least one array must be provided")
@@ -448,10 +451,7 @@ async def group(
         The new group.
     """
 
-    zarr_format = (
-        _handle_zarr_version_or_format(zarr_version=zarr_version, zarr_format=zarr_format)
-        or _default_zarr_version()
-    )
+    zarr_format = _handle_zarr_version_or_format(zarr_version=zarr_version, zarr_format=zarr_format)
 
     store_path = await make_store_path(store)
     if path is not None:
@@ -474,7 +474,7 @@ async def group(
     except (KeyError, FileNotFoundError):
         return await AsyncGroup.create(
             store=store_path,
-            zarr_format=zarr_format,
+            zarr_format=zarr_format or _default_zarr_version(),
             exists_ok=overwrite,
             attributes=attributes,
         )
@@ -483,7 +483,7 @@ async def group(
 async def open_group(
     *,  # Note: this is a change from v2
     store: StoreLike | None = None,
-    mode: AccessModeLiteral | None = None,  # not used
+    mode: AccessModeLiteral | None = None,
     cache_attrs: bool | None = None,  # not used, default changed
     synchronizer: Any = None,  # not used
     path: str | None = None,
@@ -538,10 +538,7 @@ async def open_group(
         The new group.
     """
 
-    zarr_format = (
-        _handle_zarr_version_or_format(zarr_version=zarr_version, zarr_format=zarr_format)
-        or _default_zarr_version()
-    )
+    zarr_format = _handle_zarr_version_or_format(zarr_version=zarr_version, zarr_format=zarr_format)
 
     if cache_attrs is not None:
         warnings.warn("cache_attrs is not yet implemented", RuntimeWarning, stacklevel=2)
@@ -565,7 +562,10 @@ async def open_group(
         return await AsyncGroup.open(store_path, zarr_format=zarr_format)
     except (KeyError, FileNotFoundError):
         return await AsyncGroup.create(
-            store_path, zarr_format=zarr_format, exists_ok=True, attributes=attributes
+            store_path,
+            zarr_format=zarr_format or _default_zarr_version(),
+            exists_ok=True,
+            attributes=attributes,
         )
 
 
@@ -687,7 +687,7 @@ async def create(
 
     if zarr_format == 2 and chunks is None:
         chunks = shape
-    if zarr_format == 3 and chunk_shape is None:
+    elif zarr_format == 3 and chunk_shape is None:
         if chunks is not None:
             chunk_shape = chunks
             chunks = None
@@ -908,7 +908,7 @@ async def open_array(
         if store_path.store.mode.create:
             return await create(
                 store=store_path,
-                zarr_format=zarr_format,
+                zarr_format=zarr_format or _default_zarr_version(),
                 overwrite=store_path.store.mode.overwrite,
                 **kwargs,
             )

src/zarr/core/config.py

@@ -28,21 +28,20 @@ def reset(self) -> None:
         self.refresh()
 
 
-"""
-The config module is responsible for managing the configuration of zarr and  is based on the Donfig python library.
-For selecting custom implementations of codecs, pipelines, buffers and ndbuffers, first register the implementations 
-in the registry and then select them in the config.
-e.g. an implementation of the bytes codec in a class "NewBytesCodec", requires the value of codecs.bytes.name to be 
-"NewBytesCodec".
-Donfig can be configured programmatically, by environment variables, or from YAML files in standard locations
-e.g. export ZARR_CODECS__BYTES__NAME="NewBytesCodec"
-(for more information see github.com/pytroll/donfig)
-Default values below point to the standard implementations of zarr-python
-"""
+# The config module is responsible for managing the configuration of zarr and  is based on the Donfig python library.
+# For selecting custom implementations of codecs, pipelines, buffers and ndbuffers, first register the implementations
+# in the registry and then select them in the config.
+# e.g. an implementation of the bytes codec in a class "NewBytesCodec", requires the value of codecs.bytes.name to be
+# "NewBytesCodec".
+# Donfig can be configured programmatically, by environment variables, or from YAML files in standard locations
+# e.g. export ZARR_CODECS__BYTES__NAME="NewBytesCodec"
+# (for more information see github.com/pytroll/donfig)
+# Default values below point to the standard implementations of zarr-python
 config = Config(
     "zarr",
     defaults=[
         {
+            "default_zarr_version": 3,
             "array": {"order": "C"},
             "async": {"concurrency": None, "timeout": None},
             "json_indent": 2,

tests/v3/test_api.py

@@ -8,6 +8,7 @@
 from zarr import Array, Group
 from zarr.abc.store import Store
 from zarr.api.synchronous import create, load, open, open_group, save, save_array, save_group
+from zarr.core.common import ZarrFormat
 from zarr.store.memory import MemoryStore
 
 
@@ -81,6 +82,26 @@ async def test_open_group(memory_store: MemoryStore) -> None:
     # assert g.read_only
 
 
+@pytest.mark.parametrize("zarr_format", [None, 2, 3])
+async def test_open_group_unspecified_version(
+    tmpdir: pathlib.Path, zarr_format: ZarrFormat
+) -> None:
+    """regression test for https://github.com/zarr-developers/zarr-python/issues/2175"""
+
+    # create a group with specified zarr format (could be 2, 3, or None)
+    _ = await zarr.api.asynchronous.open_group(
+        store=str(tmpdir), mode="w", zarr_format=zarr_format, attributes={"foo": "bar"}
+    )
+
+    # now open that group without specifying the format
+    g2 = await zarr.api.asynchronous.open_group(store=str(tmpdir), mode="r")
+
+    assert g2.attrs == {"foo": "bar"}
+
+    if zarr_format is not None:
+        assert g2.metadata.zarr_format == zarr_format
+
+
 def test_save_errors() -> None:
     with pytest.raises(ValueError):
         # no arrays provided

tests/v3/test_config.py

@@ -39,6 +39,7 @@ def test_config_defaults_set() -> None:
     # regression test for available defaults
     assert config.defaults == [
         {
+            "default_zarr_version": 3,
             "array": {"order": "C"},
             "async": {"concurrency": None, "timeout": None},
             "json_indent": 2,