Refactoring/fixing zarr-python v3 incompatibilities in xarray datatrees (#10020)

aladinor · pre-commit-ci[bot] · jhamman · web-flow · commit f0809e4221ed · 2025-03-20T01:01:49.000Z
* fixing compatibility with relative paths in open_store function within open_dtree for zarr * fixing/refactoring test to be compatible with Zarr-python v3 * adding @requires_zarr_v3 decorator to TestZarrDatatreeIO * replacing 0 with 1 in _create_test_datatree wich will write a chunk * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixing issues with groups * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixing issue with dict creation * fixing issues with Mypy * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * refactoring open_store in ZarrStore class to use Zarr.core.group.Group members * refactoring datree test for zarr ensuring compatibility with zarr-python v3 * importing zarr.core.group only inside open_store function * documenting changes in what's-nwe.rst file * Update xarray/backends/zarr.py Co-authored-by: Joe Hamman <jhamman1@gmail.com> * keeping grroup creation compatible with zarr v2 * fixing issue with mypy * adding root_path equal to '/' when opening group in zarr v3 to avoid ValueError: Consolidated metadata requested with 'use_consolidated=True' but not found in 'path'. * fixing tests accordingly * removing print statement * reverting changes made in unaligned test in zarr * adding requires_zarr_v3 decorator * changing max_depth=None in Group.members to get all nested groups * fixing unaligned test in datrees using zarr * Update xarray/backends/zarr.py Co-authored-by: Joe Hamman <jhamman1@gmail.com> * updating whats-new.rst entry * remove funny-looking line and refactor to ensure reading consolidated metadata * parametrize over whether or not we write consolidated metadata * fix consolidated metadata * ian hcanges * open_datatree_specific_group consolidated true works tom changes * refactoring * test: add consolidated parametrize to zarr datatree test * fix: group finding behavior consolidated * remove more debugging print statements * revert changes to test fixture * formatting * add decorator to parametrize over zarr formats * ensure both versions of zarr-python and both versions of zarr-python get tested * change datatree fixture to not produce values that would be fill_values by default in zarr * refactor test to make expected behaviour clearer * fix wrongly expected behaviour - should not expect inherited variable to be written to zarr * make arrays no longer scalars to dodge #10147 * fix bad merge * parametrize almost every test over zarr_format * parametrize encoding test over zarr_formats * use xfail in encoding test * updated expected behaviour of zarr on-disk in light of #10147 * fully revert change to simple_datatree test fixture by considered zarr's fill_value in assertion * parametrize unaligned_zarr test fixture over zarr_format * move parametrize_over_zarr_format decorator to apply to entire test class * for now explicitly consolidate metadata in test fixture * correct bug in writing of consolidated metadata * delete commented-out lines * merges from main * Revert "merges from main" This reverts commit 22ac9b4. * fix encodings test for zarr_format=3 * tidy up * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * account for different default value of write_empty_chunks between zarr-python 2 vs 3 * fix expected encoding key for compressor in zarr-python v2 * account for exception type changing * various typing fixes * remove outdated comment * bool type Co-authored-by: Deepak Cherian <dcherian@users.noreply.github.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Joe Hamman <jhamman1@gmail.com> Co-authored-by: Deepak Cherian <dcherian@users.noreply.github.com> Co-authored-by: Tom Nicholas <tom@earthmover.io> Co-authored-by: Ian Hunt-Isaak <ianhuntisaak@gmail.com>
diff --git a/doc/whats-new.rst b/doc/whats-new.rst
@@ -66,6 +66,10 @@ Deprecations
 
 Bug fixes
 ~~~~~~~~~
+
+- Fix ``open_datatree`` incompatibilities with Zarr-Python V3 and refactor
+  ``TestZarrDatatreeIO`` accordingly (:issue:`9960`, :pull:`10020`).
+  By `Alfonso Ladino-Rincon <https://github.com/aladinor>`_.
 - Default to resolution-dependent optimal integer encoding units when saving
   chunked non-nanosecond :py:class:`numpy.datetime64` or
   :py:class:`numpy.timedelta64` arrays to disk. Previously units of
@@ -97,6 +101,7 @@ Bug fixes
   datetimes and timedeltas (:issue:`8957`, :pull:`10050`).
   By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
 
+
 Documentation
 ~~~~~~~~~~~~~
 - Better expose the :py:class:`Coordinates` class in API reference (:pull:`10000`)
diff --git a/xarray/backends/zarr.py b/xarray/backends/zarr.py
@@ -666,10 +666,21 @@ def open_store(
             use_zarr_fill_value_as_mask=use_zarr_fill_value_as_mask,
             zarr_format=zarr_format,
         )
+
+        from zarr import Group
+
+        group_members: dict[str, Group] = {}
         group_paths = list(_iter_zarr_groups(zarr_group, parent=group))
-        return {
+        for path in group_paths:
+            if path == group:
+                group_members[path] = zarr_group
+            else:
+                rel_path = path.removeprefix(f"{group}/")
+                group_members[path] = zarr_group[rel_path.removeprefix("/")]
+
+        out = {
             group: cls(
-                zarr_group.get(group),
+                group_store,
                 mode,
                 consolidate_on_close,
                 append_dim,
@@ -680,8 +691,9 @@ def open_store(
                 use_zarr_fill_value_as_mask,
                 cache_members=cache_members,
             )
-            for group in group_paths
+            for group, group_store in group_members.items()
         }
+        return out
 
     @classmethod
     def open_group(
@@ -1034,8 +1046,6 @@ def store(
         if self._consolidate_on_close:
             kwargs = {}
             if _zarr_v3():
-                # https://github.com/zarr-developers/zarr-python/pull/2113#issuecomment-2386718323
-                kwargs["path"] = self.zarr_group.name.lstrip("/")
                 kwargs["zarr_format"] = self.zarr_group.metadata.zarr_format
             zarr.consolidate_metadata(self.zarr_group.store, **kwargs)
 
@@ -1662,8 +1672,6 @@ def open_groups_as_dict(
         zarr_version=None,
         zarr_format=None,
     ) -> dict[str, Dataset]:
-        from xarray.core.treenode import NodePath
-
         filename_or_obj = _normalize_path(filename_or_obj)
 
         # Check for a group and make it a parent if it exists
@@ -1686,7 +1694,6 @@ def open_groups_as_dict(
         )
 
         groups_dict = {}
-
         for path_group, store in stores.items():
             store_entrypoint = StoreBackendEntrypoint()
 
@@ -1762,44 +1769,57 @@ def _get_open_params(
             consolidated = False
 
     if _zarr_v3():
-        missing_exc = ValueError
+        # TODO: replace AssertionError after https://github.com/zarr-developers/zarr-python/issues/2821 is resolved
+        missing_exc = AssertionError
     else:
         missing_exc = zarr.errors.GroupNotFoundError
 
-    if consolidated is None:
-        try:
-            zarr_group = zarr.open_consolidated(store, **open_kwargs)
-        except (ValueError, KeyError):
-            # ValueError in zarr-python 3.x, KeyError in 2.x.
+    if consolidated in [None, True]:
+        # open the root of the store, in case there is metadata consolidated there
+        group = open_kwargs.pop("path")
+
+        if consolidated:
+            # TODO: an option to pass the metadata_key keyword
+            zarr_root_group = zarr.open_consolidated(store, **open_kwargs)
+        elif consolidated is None:
+            # same but with more error handling in case no consolidated metadata found
             try:
-                zarr_group = zarr.open_group(store, **open_kwargs)
-                emit_user_level_warning(
-                    "Failed to open Zarr store with consolidated metadata, "
-                    "but successfully read with non-consolidated metadata. "
-                    "This is typically much slower for opening a dataset. "
-                    "To silence this warning, consider:\n"
-                    "1. Consolidating metadata in this existing store with "
-                    "zarr.consolidate_metadata().\n"
-                    "2. Explicitly setting consolidated=False, to avoid trying "
-                    "to read consolidate metadata, or\n"
-                    "3. Explicitly setting consolidated=True, to raise an "
-                    "error in this case instead of falling back to try "
-                    "reading non-consolidated metadata.",
-                    RuntimeWarning,
-                )
-            except missing_exc as err:
-                raise FileNotFoundError(
-                    f"No such file or directory: '{store}'"
-                ) from err
-    elif consolidated:
-        # TODO: an option to pass the metadata_key keyword
-        zarr_group = zarr.open_consolidated(store, **open_kwargs)
+                zarr_root_group = zarr.open_consolidated(store, **open_kwargs)
+            except (ValueError, KeyError):
+                # ValueError in zarr-python 3.x, KeyError in 2.x.
+                try:
+                    zarr_root_group = zarr.open_group(store, **open_kwargs)
+                    emit_user_level_warning(
+                        "Failed to open Zarr store with consolidated metadata, "
+                        "but successfully read with non-consolidated metadata. "
+                        "This is typically much slower for opening a dataset. "
+                        "To silence this warning, consider:\n"
+                        "1. Consolidating metadata in this existing store with "
+                        "zarr.consolidate_metadata().\n"
+                        "2. Explicitly setting consolidated=False, to avoid trying "
+                        "to read consolidate metadata, or\n"
+                        "3. Explicitly setting consolidated=True, to raise an "
+                        "error in this case instead of falling back to try "
+                        "reading non-consolidated metadata.",
+                        RuntimeWarning,
+                    )
+                except missing_exc as err:
+                    raise FileNotFoundError(
+                        f"No such file or directory: '{store}'"
+                    ) from err
+
+        # but the user should still receive a DataTree whose root is the group they asked for
+        if group and group != "/":
+            zarr_group = zarr_root_group[group.removeprefix("/")]
+        else:
+            zarr_group = zarr_root_group
     else:
         if _zarr_v3():
             # we have determined that we don't want to use consolidated metadata
             # so we set that to False to avoid trying to read it
             open_kwargs["use_consolidated"] = False
         zarr_group = zarr.open_group(store, **open_kwargs)
+
     close_store_on_close = zarr_group.store is not store
 
     # we use this to determine how to handle fill_value
diff --git a/xarray/core/datatree.py b/xarray/core/datatree.py
@@ -16,7 +16,6 @@
     TYPE_CHECKING,
     Any,
     Concatenate,
-    Literal,
     NoReturn,
     ParamSpec,
     TypeVar,
@@ -1741,7 +1740,7 @@ def to_zarr(
         consolidated: bool = True,
         group: str | None = None,
         write_inherited_coords: bool = False,
-        compute: Literal[True] = True,
+        compute: bool = True,
         **kwargs,
     ):
         """
diff --git a/xarray/tests/__init__.py b/xarray/tests/__init__.py
@@ -165,6 +165,21 @@ def _importorskip(
 
 has_array_api_strict, requires_array_api_strict = _importorskip("array_api_strict")
 
+parametrize_zarr_format = pytest.mark.parametrize(
+    "zarr_format",
+    [
+        pytest.param(2, id="zarr_format=2"),
+        pytest.param(
+            3,
+            marks=pytest.mark.skipif(
+                not has_zarr_v3,
+                reason="zarr-python v2 cannot understand the zarr v3 format",
+            ),
+            id="zarr_format=3",
+        ),
+    ],
+)
+
 
 def _importorskip_h5netcdf_ros3(has_h5netcdf: bool):
     if not has_h5netcdf:
diff --git a/xarray/tests/test_backends_datatree.py b/xarray/tests/test_backends_datatree.py
