From 439accd6e0aa0098ef3af7122792b61d3e30d08e Mon Sep 17 00:00:00 2001
From: Max Jones <14077947+maxrjones@users.noreply.github.com>
Date: Tue, 11 Nov 2025 12:44:01 -0500
Subject: [PATCH 1/7] Return None for Zarr V2/consolidated metadata requests

---
 virtualizarr/manifests/store.py                  |  6 ++++++
 .../test_hdf/test_hdf_manifest_store.py          | 16 ++++++++++++++++
 2 files changed, 22 insertions(+)

diff --git a/virtualizarr/manifests/store.py b/virtualizarr/manifests/store.py
index 962c122e..2c301447 100644
--- a/virtualizarr/manifests/store.py
+++ b/virtualizarr/manifests/store.py
@@ -171,6 +171,12 @@ async def get(
             return self._group.arrays[var].metadata.to_buffer_dict(
                 prototype=default_buffer_prototype()
             )["zarr.json"]
+        elif key.endswith((".zattrs", ".zgroup", ".zarray", ".zmetadata")):
+            # Zarr-Python expects store classes to return None when metadata JSONs are not found.
+            # Zarr-Python uses this behavior to distinguish between V2/V3 and consolidated/unconsolidated stores.
+            # This upstream behavior will hopefully change in the future to be more Zarr-hierarchy aware, in
+            # which case this may need refactoring.
+            return None
         var = key.split("/")[0]
         marr = self._group.arrays[var]
         manifest = marr.manifest
diff --git a/virtualizarr/tests/test_parsers/test_hdf/test_hdf_manifest_store.py b/virtualizarr/tests/test_parsers/test_hdf/test_hdf_manifest_store.py
index 3194e8db..32046f0e 100644
--- a/virtualizarr/tests/test_parsers/test_hdf/test_hdf_manifest_store.py
+++ b/virtualizarr/tests/test_parsers/test_hdf/test_hdf_manifest_store.py
@@ -42,6 +42,22 @@ def test_roundtrip_simple_virtualdataset(self, tmpdir, basic_ds):
         ) as rountripped_ds:
             xr.testing.assert_allclose(basic_ds, rountripped_ds)
 
+    def test_roundtrip_simple_virtualdataset_guess_zarr_format(self, tmpdir, basic_ds):
+        """
+        Roundtrip a dataset to/from NetCDF with the HDF reader and ManifestStore, relying
+        on xarray/zarr to guess the zarr format and unconsolidated store metadata.
+        """
+
+        filepath = f"{tmpdir}/basic_ds_roundtrip.nc"
+        url = f"file://{filepath}"
+        basic_ds.to_netcdf(filepath, engine="h5netcdf")
+        manifest_store = manifest_store_from_hdf_url(url)
+        with xr.open_dataset(
+            manifest_store,
+            engine="zarr",
+        ) as rountripped_ds:
+            xr.testing.assert_allclose(basic_ds, rountripped_ds)
+
     def test_rountrip_partial_chunk_virtualdataset(self, tmpdir, basic_ds):
         "Roundtrip a dataset to/from NetCDF with the HDF reader and ManifestStore with a single partial chunk"
 

From 24e29f38d518bd5059de1102e55f47e97ead9cf9 Mon Sep 17 00:00:00 2001
From: Max Jones <14077947+maxrjones@users.noreply.github.com>
Date: Tue, 11 Nov 2025 14:11:46 -0500
Subject: [PATCH 2/7] Squashed commit of the following:

commit 113c71285534f8c39c56ca40e117bd946b9e9c51
Author: Ilan Gold <ilanbassgold@gmail.com>
Date:   Tue Nov 11 17:25:49 2025 +0100

    Update virtualizarr/tests/test_parsers/test_hdf/test_hdf.py

    Co-authored-by: Chuck Daniels <cjdaniels4@gmail.com>

commit 56936491db174faeae97e97635c8522218e7f172
Author: Ilan Gold <ilanbassgold@gmail.com>
Date:   Tue Nov 11 17:25:10 2025 +0100

    refactor: `get_deepest_group_or_array` type

commit 849d5677462261f9e446cec870619f72aa5f7a15
Merge: 916c3e1 7a13261
Author: Ilan Gold <ilanbassgold@gmail.com>
Date:   Fri Nov 7 14:18:51 2025 +0100

    Merge branch 'main' into ig/nested_h5_group

commit 916c3e17f05fd0d90520784ba79260ac61279264
Merge: d8dc369 a2b65c1
Author: Ilan Gold <ilanbassgold@gmail.com>
Date:   Wed Sep 10 13:11:01 2025 +0200

    Merge branch 'main' into ig/nested_h5_group

commit d8dc36973e66c1c75eb713d03a0028119b0dda84
Author: Ilan Gold <ilanbassgold@gmail.com>
Date:   Sun Sep 7 19:53:08 2025 +0200

    fix: update release note

commit a3a26153da2644acf7c2e6396f05f6d2e7b98944
Author: ilan-gold <ilanbassgold@gmail.com>
Date:   Sun Sep 7 16:45:22 2025 +0200

    chore: clean up error handling for non-metadata group requests + tests

commit fc0e99952ca3f2aadb399d39b127fdf0ff3967a4
Merge: 3036de8 1facb10
Author: ilan-gold <ilanbassgold@gmail.com>
Date:   Sun Sep 7 16:29:59 2025 +0200

    Merge branch 'ig/nested_h5_group' of https://github.com/ilan-gold/VirtualiZarr into ig/nested_h5_group

commit 3036de8911bbdf445fb4aa927a2034dec6aa28a4
Author: ilan-gold <ilanbassgold@gmail.com>
Date:   Sun Sep 7 16:29:44 2025 +0200

    fix: remove subgroup check

commit 1facb107127874ca5aac8e274e027ab7abc5b783
Author: Ilan Gold <ilanbassgold@gmail.com>
Date:   Sun Sep 7 16:17:43 2025 +0200

    fix: wrong place!

commit 33e517e84c2dce700c2f4f6e147d4f060f9447ac
Merge: afcaaed c1db925
Author: Ilan Gold <ilanbassgold@gmail.com>
Date:   Sun Sep 7 16:17:21 2025 +0200

    Merge branch 'main' into ig/nested_h5_group

commit afcaaedb7d0bb2400f3836dda029d10a2853dfbd
Author: ilan-gold <ilanbassgold@gmail.com>
Date:   Sun Sep 7 16:15:26 2025 +0200

    chore: consolidate tests

commit 253d184ddb0c8c15f1376c392f18d339981b3b13
Author: ilan-gold <ilanbassgold@gmail.com>
Date:   Sun Sep 7 15:57:18 2025 +0200

    fix: disallow nested xarray handling

commit 57551b893eb08b342507d172891221c2bcbcc26b
Author: ilan-gold <ilanbassgold@gmail.com>
Date:   Fri Aug 29 08:52:28 2025 +0200

    chore: relnote

commit 6fe1dbd0773aa860f2c3cc551197c0abed915c76
Author: ilan-gold <ilanbassgold@gmail.com>
Date:   Fri Aug 29 08:45:57 2025 +0200

    fix: typing

commit 85f2930d11f02d8eabd8453b0e440571ac8a6cef
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Thu Aug 28 16:27:24 2025 +0000

    [pre-commit.ci] auto fixes from pre-commit.com hooks

    for more information, see https://pre-commit.ci

commit e92ba8cf39be7faed44a29a542891fba595bb829
Author: ilan-gold <ilanbassgold@gmail.com>
Date:   Thu Aug 28 18:19:46 2025 +0200

    fix: simplify node logic

commit 323be331d98d8aae53ddbab33c4113c60f9dcd83
Author: ilan-gold <ilanbassgold@gmail.com>
Date:   Thu Aug 28 18:02:04 2025 +0200

    feat: nested groups
---
 docs/releases.md                              |  4 ++
 virtualizarr/manifests/group.py               |  8 +---
 virtualizarr/manifests/store.py               | 40 +++++++++++--------
 virtualizarr/parsers/hdf/hdf.py               | 17 ++++++--
 .../tests/test_manifests/test_store.py        | 24 +++++++++--
 virtualizarr/tests/test_parsers/conftest.py   |  3 +-
 .../tests/test_parsers/test_hdf/test_hdf.py   | 20 +++++++++-
 virtualizarr/xarray.py                        |  1 +
 8 files changed, 85 insertions(+), 32 deletions(-)

diff --git a/docs/releases.md b/docs/releases.md
index 092622da..55f98b06 100644
--- a/docs/releases.md
+++ b/docs/releases.md
@@ -4,6 +4,10 @@
 
 ### New Features
 
+- Allow nested-groups inside `ManifestStore` and `ManifestGroup` objects and update `HDFParser` to be able to create nested `zarr.Group` objects.
+  ([#790](https://github.com/zarr-developers/VirtualiZarr/pull/790)).
+  By [Ilan Gold](https://github.com/ilan-gold)
+
 ### Breaking changes
 
 ### Bug fixes
diff --git a/virtualizarr/manifests/group.py b/virtualizarr/manifests/group.py
index c3caf685..7f637fcf 100644
--- a/virtualizarr/manifests/group.py
+++ b/virtualizarr/manifests/group.py
@@ -40,13 +40,7 @@ def __init__(
         self._metadata = GroupMetadata(attributes=attributes)
 
         _arrays: Mapping[str, ManifestArray] = {} if arrays is None else arrays
-
-        if groups:
-            # TODO add support for nested groups
-            raise NotImplementedError
-        else:
-            _groups: Mapping[str, ManifestGroup] = {} if groups is None else groups
-
+        _groups: Mapping[str, ManifestGroup] = {} if groups is None else groups
         for name, arr in _arrays.items():
             if not isinstance(arr, ManifestArray):
                 raise TypeError(
diff --git a/virtualizarr/manifests/store.py b/virtualizarr/manifests/store.py
index 2c301447..de1c93fb 100644
--- a/virtualizarr/manifests/store.py
+++ b/virtualizarr/manifests/store.py
@@ -16,6 +16,7 @@
 from zarr.core.buffer import Buffer, BufferPrototype, default_buffer_prototype
 from zarr.core.common import BytesLike
 
+from virtualizarr.manifests.array import ManifestArray
 from virtualizarr.manifests.group import ManifestGroup
 from virtualizarr.manifests.utils import construct_chunk_pattern
 from virtualizarr.registry import ObjectStoreRegistry
@@ -97,6 +98,16 @@ def parse_manifest_index(
     return tuple(int(ind) for ind in chunk_component.split(chunk_key_encoding))
 
 
+def get_deepest_group_or_array(
+    node: ManifestGroup, key: Iterable[str]
+) -> ManifestGroup | ManifestArray:
+    for var in key:
+        if var in node.arrays:
+            return node.arrays[var]
+        node = node.groups[var]
+    return node
+
+
 class ManifestStore(Store):
     """
     A read-only Zarr store that uses obstore to read data from inside arbitrary files on AWS, GCP, Azure, or a local filesystem.
@@ -158,31 +169,26 @@ async def get(
         byte_range: ByteRequest | None = None,
     ) -> Buffer | None:
         # docstring inherited
-
-        if key == "zarr.json":
-            # Return group metadata
-            return self._group.metadata.to_buffer_dict(
-                prototype=default_buffer_prototype()
-            )["zarr.json"]
-        elif key.endswith("zarr.json"):
-            # Return array metadata
-            # TODO: Handle nested groups
-            var, _ = key.split("/")
-            return self._group.arrays[var].metadata.to_buffer_dict(
-                prototype=default_buffer_prototype()
-            )["zarr.json"]
+        node = get_deepest_group_or_array(self._group, key.split("/")[:-1])
+        if key.endswith("zarr.json"):
+            # Return metadata
+            return node.metadata.to_buffer_dict(prototype=default_buffer_prototype())[
+                "zarr.json"
+            ]
         elif key.endswith((".zattrs", ".zgroup", ".zarray", ".zmetadata")):
             # Zarr-Python expects store classes to return None when metadata JSONs are not found.
             # Zarr-Python uses this behavior to distinguish between V2/V3 and consolidated/unconsolidated stores.
             # This upstream behavior will hopefully change in the future to be more Zarr-hierarchy aware, in
             # which case this may need refactoring.
             return None
-        var = key.split("/")[0]
-        marr = self._group.arrays[var]
-        manifest = marr.manifest
+        if isinstance(node, ManifestGroup):
+            raise ValueError(
+                "Key requested is a group but the key does not end in `zarr.json`"
+            )
+        manifest = node.manifest
 
         separator: Literal[".", "/"] = getattr(
-            marr.metadata.chunk_key_encoding, "separator", "."
+            node.metadata.chunk_key_encoding, "separator", "."
         )
         chunk_indexes = parse_manifest_index(key, separator)
 
diff --git a/virtualizarr/parsers/hdf/hdf.py b/virtualizarr/parsers/hdf/hdf.py
index c3968de6..1943bf58 100644
--- a/virtualizarr/parsers/hdf/hdf.py
+++ b/virtualizarr/parsers/hdf/hdf.py
@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 import math
+from pathlib import Path
 from typing import (
     TYPE_CHECKING,
     Iterable,
@@ -98,7 +99,6 @@ def _construct_manifest_group(
     """
     Construct a virtual Group from a HDF dataset.
     """
-
     import h5py
 
     with h5py.File(reader, mode="r") as f:
@@ -116,11 +116,22 @@ def _construct_manifest_group(
         arrays = {
             key: _construct_manifest_array(filepath, dataset, group_name)
             for key in g.keys()
-            if key not in drop_variables and isinstance(dataset := g[key], h5py.Dataset)
+            if key not in drop_variables
+            if isinstance(dataset := g[key], h5py.Dataset)
+        }
+        groups = {
+            key: _construct_manifest_group(
+                filepath,
+                reader,
+                group=str(Path(group) / key) if group is not None else key,
+            )
+            for key in g.keys()
+            if key not in drop_variables
+            if isinstance(g[key], h5py.Group)
         }
         attributes = _extract_attrs(g)
 
-    return ManifestGroup(arrays=arrays, attributes=attributes)
+    return ManifestGroup(arrays=arrays, groups=groups, attributes=attributes)
 
 
 class HDFParser:
diff --git a/virtualizarr/tests/test_manifests/test_store.py b/virtualizarr/tests/test_manifests/test_store.py
index 033dc528..2e571725 100644
--- a/virtualizarr/tests/test_manifests/test_store.py
+++ b/virtualizarr/tests/test_manifests/test_store.py
@@ -145,6 +145,7 @@ def _generate_manifest_store(
             "bar": manifest_array,
             "scalar": scalar_manifest_array,
         },
+        groups={"subgroup": ManifestGroup(arrays={"foo": manifest_array})},
         attributes={"Zarr": "Hooray!"},
     )
     registry = ObjectStoreRegistry({prefix: store})
@@ -205,7 +206,10 @@ def empty_memory_store():
         fill_value=0,
     )
     manifest_array = ManifestArray(metadata=array_metadata, chunkmanifest=manifest)
-    manifest_group = ManifestGroup(arrays={"foo": manifest_array})
+    sub_group = ManifestGroup(arrays={"foo": manifest_array})
+    manifest_group = ManifestGroup(
+        arrays={"foo": manifest_array}, groups={"subgroup": sub_group}
+    )
     registry = ObjectStoreRegistry({"memory://": store})
     return ManifestStore(registry=registry, group=manifest_group)
 
@@ -229,6 +233,16 @@ async def test_get_empty_chunk(self, manifest_store, request):
         observed = await store.get("foo/c.0.0", prototype=default_buffer_prototype())
         assert observed is None
 
+    @pytest.mark.asyncio
+    @pytest.mark.parametrize(
+        "manifest_store",
+        ["empty_memory_store"],
+    )
+    async def test_get_group_key_fails(self, manifest_store, request):
+        store = request.getfixturevalue(manifest_store)
+        with pytest.raises(ValueError, match=r"Key requested is a group"):
+            await store.get("subgroup", prototype=default_buffer_prototype())
+
     @pytest.mark.asyncio
     @pytest.mark.parametrize(
         "manifest_store",
@@ -269,10 +283,14 @@ async def test_get_data(self, manifest_store, request):
         "manifest_store",
         ["local_store", pytest.param("s3_store", marks=requires_minio)],
     )
-    async def test_get_metadata(self, manifest_store, request):
+    @pytest.mark.parametrize(
+        "subgroup",
+        ["", "subgroup/"],
+    )
+    async def test_get_metadata(self, manifest_store, request, subgroup):
         store = request.getfixturevalue(manifest_store)
         observed = await store.get(
-            "foo/zarr.json", prototype=default_buffer_prototype()
+            f"{subgroup}foo/zarr.json", prototype=default_buffer_prototype()
         )
         metadata = json.loads(observed.to_bytes())
         assert metadata["chunk_grid"]["configuration"]["chunk_shape"] == [2, 2]
diff --git a/virtualizarr/tests/test_parsers/conftest.py b/virtualizarr/tests/test_parsers/conftest.py
index 02db235a..83e44e8e 100644
--- a/virtualizarr/tests/test_parsers/conftest.py
+++ b/virtualizarr/tests/test_parsers/conftest.py
@@ -151,7 +151,8 @@ def nested_group_hdf5_url(tmp_path: Path) -> str:
         g = f.create_group("group")
         data = np.random.random((10, 10))
         g.create_dataset("data", data=data)
-        g.create_group("nested_group")
+        g_nested = g.create_group("nested_group")
+        g_nested.create_dataset("data", data=data)
 
     return f"file://{filepath}"
 
diff --git a/virtualizarr/tests/test_parsers/test_hdf/test_hdf.py b/virtualizarr/tests/test_parsers/test_hdf/test_hdf.py
index 114ed718..f0e04594 100644
--- a/virtualizarr/tests/test_parsers/test_hdf/test_hdf.py
+++ b/virtualizarr/tests/test_parsers/test_hdf/test_hdf.py
@@ -2,6 +2,7 @@
 import numpy as np
 import pytest
 import xarray as xr
+import zarr
 from obstore.store import from_url
 
 from virtualizarr import open_virtual_dataset
@@ -129,12 +130,29 @@ def test_variable_with_dimensions(self, chunked_dimensions_netcdf4_url):
         manifest_store = manifest_store_from_hdf_url(chunked_dimensions_netcdf4_url)
         assert len(manifest_store._group.arrays) == 3
 
-    def test_nested_groups_are_ignored(self, nested_group_hdf5_url):
+    def test_nested_groups_are_ignored_when_group_is_specificed(
+        self, nested_group_hdf5_url
+    ):
         manifest_store = manifest_store_from_hdf_url(
             nested_group_hdf5_url, group="group"
         )
         assert len(manifest_store._group.arrays) == 1
 
+    def test_nested_groups_are_detected(self, nested_group_hdf5_url):
+        manifest_store = manifest_store_from_hdf_url(nested_group_hdf5_url)
+        assert len(manifest_store._group["group"]["nested_group"].arrays) == 1
+
+    def test_nested_data(self, nested_group_hdf5_url):
+        manifest_store = manifest_store_from_hdf_url(nested_group_hdf5_url)
+        z = zarr.open_group(manifest_store, mode="r", zarr_format=3)
+
+        with h5py.File(nested_group_hdf5_url.removeprefix("file://"), mode="r") as f:
+            np.testing.assert_array_equal(f["group"]["data"], z["group"]["data"][...])
+            np.testing.assert_array_equal(
+                f["group"]["nested_group"]["data"][...],
+                z["group"]["nested_group"]["data"][...],
+            )
+
     def test_drop_variables(self, multiple_datasets_hdf5_url, local_registry):
         parser = HDFParser(drop_variables=["data2"])
         manifest_store = parser(url=multiple_datasets_hdf5_url, registry=local_registry)
diff --git a/virtualizarr/xarray.py b/virtualizarr/xarray.py
index 3634c524..bcd63b20 100644
--- a/virtualizarr/xarray.py
+++ b/virtualizarr/xarray.py
@@ -333,6 +333,7 @@ def construct_virtual_dataset(
 
     """
 
+    # TODO: Remove private API `._group`
     if group:
         raise NotImplementedError("ManifestStore does not yet support nested groups")
     else:

From 1e1db55fbca2dee6d9262e47c7cc8ca628fc07cc Mon Sep 17 00:00:00 2001
From: Max Jones <14077947+maxrjones@users.noreply.github.com>
Date: Thu, 13 Nov 2025 18:49:11 -0500
Subject: [PATCH 3/7] Squashed commit of the following:

commit 128138b45212af069f4e0c4bd1d7766c863ed20b
Author: Max Jones <14077947+maxrjones@users.noreply.github.com>
Date:   Thu Nov 13 18:39:24 2025 -0500

    Apply suggestion from code review

commit 9c0e8032cc55affcd57b764270db98fbbde25de0
Author: Max Jones <14077947+maxrjones@users.noreply.github.com>
Date:   Thu Nov 13 18:25:39 2025 -0500

    Apply suggestions from code review

    Co-authored-by: Chuck Daniels <cjdaniels4@gmail.com>

commit d1595b4d05dd5a671b69a247da35d7806f00ade3
Author: Max Jones <14077947+maxrjones@users.noreply.github.com>
Date:   Thu Nov 13 18:25:10 2025 -0500

    Update virtualizarr/manifests/store.py

    Co-authored-by: Chuck Daniels <cjdaniels4@gmail.com>

commit 15739922e5f95235030cd2536d5a8027e8358a3b
Author: Max Jones <14077947+maxrjones@users.noreply.github.com>
Date:   Thu Nov 13 18:17:32 2025 -0500

    Add test for listing array in subgroup

commit dcf80bbcb0135ca7ab955554d6173f4405fbbcbd
Author: Max Jones <14077947+maxrjones@users.noreply.github.com>
Date:   Thu Nov 13 15:25:10 2025 -0500

    Fix typing

commit 2448c5df9bfe7d62290d1bc796965f314a29d2cc
Author: Max Jones <14077947+maxrjones@users.noreply.github.com>
Date:   Thu Nov 13 15:08:33 2025 -0500

    Improve ManifestStore.list_dir for arrays and nested groups
---
 virtualizarr/manifests/store.py               | 79 +++++++++++++++----
 .../tests/test_manifests/test_store.py        | 10 ++-
 2 files changed, 72 insertions(+), 17 deletions(-)

diff --git a/virtualizarr/manifests/store.py b/virtualizarr/manifests/store.py
index 895af001..874a253e 100644
--- a/virtualizarr/manifests/store.py
+++ b/virtualizarr/manifests/store.py
@@ -80,7 +80,7 @@ def parse_manifest_index(
     """
     # Keys ending in `/c` are scalar arrays. The paths, offsets, and lengths in a chunk manifest
     # of a scalar array should also be scalar arrays that can be indexed with an empty tuple.
-    if key.endswith("/c"):
+    if key.endswith("/c") or key == "c":
         return ()
 
     pattern = construct_chunk_pattern(chunk_key_encoding)
@@ -98,14 +98,33 @@ def parse_manifest_index(
     return tuple(int(ind) for ind in chunk_component.split(chunk_key_encoding))
 
 
-def get_deepest_group_or_array(
-    node: ManifestGroup, key: Iterable[str]
-) -> ManifestGroup | ManifestArray:
-    for var in key:
-        if var in node.arrays:
-            return node.arrays[var]
-        node = node.groups[var]
-    return node
+def _get_deepest_group_or_array(
+    node: ManifestGroup, key: str
+) -> tuple[ManifestGroup | ManifestArray, str]:
+    """
+    Traverse the manifest hierarchy as deeply as possible following the given key path.
+
+    Traversal stops when:
+    - A key part doesn't match any array or group in the current node
+    - A ManifestArray is reached (arrays cannot be traversed further)
+    - All key parts have been successfully matched
+
+    Args:
+        node: The starting ManifestGroup to begin traversal from
+        key: The key to use to traverse through groups and arrays
+
+    Returns:
+        A tuple containing:
+        - The deepest node reached (ManifestGroup or ManifestArray)
+        - String with remaining unmatched key portion
+    """
+    var, suffix = key.split("/", 1) if "/" in key else (key, "")
+    if var in node.arrays:
+        return node.arrays[var], suffix
+    if var in node.groups:
+        return _get_deepest_group_or_array(node.groups[var], suffix)
+    # Can't traverse deeper - return last node and remainder
+    return node, suffix or var
 
 
 class ManifestStore(Store):
@@ -169,13 +188,13 @@ async def get(
         byte_range: ByteRequest | None = None,
     ) -> Buffer | None:
         # docstring inherited
-        node = get_deepest_group_or_array(self._group, key.split("/")[:-1])
-        if key.endswith("zarr.json"):
+        node, suffix = _get_deepest_group_or_array(self._group, key)
+        if suffix.endswith("zarr.json"):
             # Return metadata
             return node.metadata.to_buffer_dict(prototype=default_buffer_prototype())[
                 "zarr.json"
             ]
-        elif key.endswith((".zattrs", ".zgroup", ".zarray", ".zmetadata")):
+        elif suffix.endswith((".zattrs", ".zgroup", ".zarray", ".zmetadata")):
             # Zarr-Python expects store classes to return None when metadata JSONs are not found.
             # Zarr-Python uses this behavior to distinguish between V2/V3 and consolidated/unconsolidated stores.
             # This upstream behavior will hopefully change in the future to be more Zarr-hierarchy aware, in
@@ -190,7 +209,7 @@ async def get(
         separator: Literal[".", "/"] = getattr(
             node.metadata.chunk_key_encoding, "separator", "."
         )
-        chunk_indexes = parse_manifest_index(key, separator)
+        chunk_indexes = parse_manifest_index(suffix, separator)
 
         path = manifest._paths[chunk_indexes]
         if path == "":
@@ -286,9 +305,37 @@ def list_prefix(self, prefix: str) -> AsyncGenerator[str, None]:
 
     async def list_dir(self, prefix: str) -> AsyncGenerator[str, None]:
         # docstring inherited
-        yield "zarr.json"
-        for k in self._group.arrays.keys():
-            yield k
+        # Navigate to the target node
+        node, suffix = _get_deepest_group_or_array(self._group, prefix)
+        # Zarr-Python lists using a per-path basis, so we don't have anything to list
+        # as long as there is a suffix remaining and we require a '.' chunk separator in the ManifestArrays
+        if suffix:
+            return
+        # List contents based on node type
+        if isinstance(node, ManifestGroup):
+            # Groups contain a metadata document and the name of sub-groups/arrays
+            yield "zarr.json"
+            for member_name in node._members.keys():
+                yield member_name
+        # TODO: Support listing when using other chunk_key_encodings
+        elif (
+            separator := getattr(node.metadata.chunk_key_encoding, "separator", None)
+            != "."
+        ):
+            raise NotImplementedError(
+                f"Array listing only supports '.' as chunk key separator, "
+                f"got {separator!r}"
+            )
+        else:
+            # Arrays contain a metadata document and chunks
+            yield "zarr.json"
+            if node.shape == ():
+                # Scalar arrays have a single chunk named 'c'
+                yield "c"
+            else:
+                # Multi-dimensional arrays have chunks named 'c.{key}'
+                for chunk_key in node.manifest.keys():
+                    yield f"c.{chunk_key}"
 
     def to_virtual_dataset(
         self,
diff --git a/virtualizarr/tests/test_manifests/test_store.py b/virtualizarr/tests/test_manifests/test_store.py
index 2e571725..0fc11168 100644
--- a/virtualizarr/tests/test_manifests/test_store.py
+++ b/virtualizarr/tests/test_manifests/test_store.py
@@ -326,7 +326,15 @@ async def test_pickling(self, local_store):
     async def test_list_dir(self, manifest_store, request) -> None:
         store = request.getfixturevalue(manifest_store)
         observed = await _collect_aiterator(store.list_dir(""))
-        assert observed == ("zarr.json", "foo", "bar", "scalar")
+        assert observed == ("zarr.json", "foo", "bar", "scalar", "subgroup")
+        observed = await _collect_aiterator(store.list_dir("scalar"))
+        assert observed == ("zarr.json", "c")
+        observed = await _collect_aiterator(store.list_dir("scalar/d"))
+        assert observed == ()
+        observed = await _collect_aiterator(store.list_dir("foo/"))
+        assert observed == ("zarr.json", "c.0.0", "c.0.1", "c.1.0", "c.1.1")
+        observed = await _collect_aiterator(store.list_dir("subgroup/foo/"))
+        assert observed == ("zarr.json", "c.0.0", "c.0.1", "c.1.0", "c.1.1")
 
     @pytest.mark.asyncio
     async def test_store_raises(self, local_store) -> None:

From 437a5d87f1d3d74dfe57988ab57d1ab4be36ccf8 Mon Sep 17 00:00:00 2001
From: Max Jones <14077947+maxrjones@users.noreply.github.com>
Date: Fri, 14 Nov 2025 12:31:40 -0500
Subject: [PATCH 4/7] Feat: add top-level open_virtual_datatree

---
 pyproject.toml                               |   1 +
 virtualizarr/__init__.py                     |   7 +-
 virtualizarr/manifests/group.py              |  32 ++++++
 virtualizarr/manifests/store.py              |  40 ++++++++
 virtualizarr/tests/test_parsers/test_tiff.py |  24 ++++-
 virtualizarr/xarray.py                       | 102 ++++++++++++++++++-
 6 files changed, 201 insertions(+), 5 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 9108b15a..898c7da6 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -101,6 +101,7 @@ upstream = [
     's3fs @ git+https://github.com/fsspec/s3fs',
     'kerchunk @ git+https://github.com/fsspec/kerchunk',
     'icechunk @ git+https://github.com/earth-mover/icechunk#subdirectory=icechunk-python',
+    'virtual_tiff @ git+https://github.com/virtual-zarr/virtual-tiff',
 ]
 docs = [
     "mkdocs-material[imaging]>=9.6.14",
diff --git a/virtualizarr/__init__.py b/virtualizarr/__init__.py
index 34264206..8ffc6e71 100644
--- a/virtualizarr/__init__.py
+++ b/virtualizarr/__init__.py
@@ -4,7 +4,11 @@
     VirtualiZarrDatasetAccessor,
     VirtualiZarrDataTreeAccessor,
 )
-from virtualizarr.xarray import open_virtual_dataset, open_virtual_mfdataset
+from virtualizarr.xarray import (
+    open_virtual_dataset,
+    open_virtual_datatree,
+    open_virtual_mfdataset,
+)
 
 try:
     __version__ = _version("virtualizarr")
@@ -18,4 +22,5 @@
     "VirtualiZarrDataTreeAccessor",
     "open_virtual_dataset",
     "open_virtual_mfdataset",
+    "open_virtual_datatree",
 ]
diff --git a/virtualizarr/manifests/group.py b/virtualizarr/manifests/group.py
index 7f637fcf..3a5a6091 100644
--- a/virtualizarr/manifests/group.py
+++ b/virtualizarr/manifests/group.py
@@ -75,6 +75,11 @@ def groups(self) -> dict[str, "ManifestGroup"]:
         """Subgroups contained in this group."""
         return {k: v for k, v in self._members.items() if isinstance(v, ManifestGroup)}
 
+    @property
+    def contains_groups(self) -> bool:
+        """True if this group has subgroups."""
+        return any(isinstance(v, ManifestGroup) for v in self._members.values())
+
     def __getitem__(self, path: str) -> "ManifestArray | ManifestGroup":
         """Obtain a group member."""
         if "/" in path:
@@ -125,3 +130,30 @@ def to_virtual_dataset(self) -> xr.Dataset:
             coord_names=coord_names,
             attrs=attributes,
         )
+
+    def to_virtual_datasets(self) -> dict[str, xr.Dataset]:
+        """
+        Create a "virtual" [xarray.DataTree][] containing the contents of one zarr group.
+
+        All variables in the returned DataTree will be "virtual", i.e. they will wrap ManifestArray objects.
+        """
+        result = {"": self.to_virtual_dataset()}
+
+        # Recursively process all subgroups
+        for group_name, subgroup in self.groups.items():
+            subgroup_datasets = subgroup.to_virtual_datasets()
+
+            # Add the subgroup's datasets with proper path prefixes
+            for subpath, dataset in subgroup_datasets.items():
+                if subpath == "":
+                    # Direct child group
+                    full_path = group_name
+                else:
+                    # Nested subgroup
+                    full_path = f"{group_name}/{subpath}"
+                result[full_path] = dataset
+        return result
+
+    def to_virtual_datatree(self) -> xr.DataTree:
+        datasets = self.to_virtual_datasets()
+        return xr.DataTree.from_dict(datasets)
diff --git a/virtualizarr/manifests/store.py b/virtualizarr/manifests/store.py
index 874a253e..d72b70e7 100644
--- a/virtualizarr/manifests/store.py
+++ b/virtualizarr/manifests/store.py
@@ -374,6 +374,46 @@ def to_virtual_dataset(
             decode_times=decode_times,
         )
 
+    def to_virtual_datatree(
+        self,
+        group="",
+        *,
+        drop_variables: Iterable[str] | None = None,
+        loadable_variables: Iterable[str] | None = None,
+        decode_times: bool | None = None,
+    ) -> "xr.DataTree":
+        """
+        Create a "virtual" [xarray.Datatree][] containing the contents of a zarr group. Default is the root group and all sub-groups.
+
+        Will ignore the contents of any other groups in the store.
+
+        Requires xarray.
+
+        Parameters
+        ----------
+        group : Group to convert to a virtual DataTree
+        drop_variables
+            Variables in the data source to drop before returning.
+        loadable_variables
+            Variables in the data source to load as Dask/NumPy arrays instead of as virtual arrays.
+        decode_times
+            Bool that is passed into [xarray.open_dataset][]. Allows time to be decoded into a datetime object.
+
+        Returns
+        -------
+        vdt : xarray.Datatree
+        """
+
+        from virtualizarr.xarray import construct_virtual_datatree
+
+        return construct_virtual_datatree(
+            manifest_store=self,
+            group=group,
+            loadable_variables=loadable_variables,
+            decode_times=decode_times,
+            drop_variables=drop_variables,
+        )
+
 
 def _transform_byte_range(
     byte_range: ByteRequest | None, *, chunk_start: int, chunk_end_exclusive: int
diff --git a/virtualizarr/tests/test_parsers/test_tiff.py b/virtualizarr/tests/test_parsers/test_tiff.py
index 38ea85a0..02397c0c 100644
--- a/virtualizarr/tests/test_parsers/test_tiff.py
+++ b/virtualizarr/tests/test_parsers/test_tiff.py
@@ -1,8 +1,8 @@
 import pytest
 from obstore.store import S3Store
-from xarray import Dataset
+from xarray import Dataset, DataTree
 
-from virtualizarr import open_virtual_dataset
+from virtualizarr import open_virtual_dataset, open_virtual_datatree
 from virtualizarr.registry import ObjectStoreRegistry
 from virtualizarr.tests import requires_network, requires_tiff
 
@@ -11,7 +11,25 @@
 
 @requires_tiff
 @requires_network
-def test_virtual_tiff() -> None:
+def test_virtual_tiff_datatree() -> None:
+    store = S3Store("sentinel-cogs", region="us-west-2", skip_signature=True)
+    registry = ObjectStoreRegistry({"s3://sentinel-cogs/": store})
+    url = "s3://sentinel-cogs/sentinel-s2-l2a-cogs/12/S/UF/2022/6/S2B_12SUF_20220609_0_L2A/B04.tif"
+    parser = virtual_tiff.VirtualTIFF(ifd_layout="nested")
+    with open_virtual_datatree(url=url, parser=parser, registry=registry) as vdt:
+        assert isinstance(vdt, DataTree)
+        assert list(vdt["0"].ds.variables) == ["0"]
+        var = vdt["0"].ds["0"].variable
+        assert var.sizes == {"y": 10980, "x": 10980}
+        assert var.dtype == "<u2"
+        var = vdt["1"].ds["1"].variable
+        assert var.sizes == {"y": 5490, "x": 5490}
+        assert var.dtype == "<u2"
+
+
+@requires_tiff
+@requires_network
+def test_virtual_tiff_dataset() -> None:
     store = S3Store("sentinel-cogs", region="us-west-2", skip_signature=True)
     registry = ObjectStoreRegistry({"s3://sentinel-cogs/": store})
     url = "s3://sentinel-cogs/sentinel-s2-l2a-cogs/12/S/UF/2022/6/S2B_12SUF_20220609_0_L2A/B04.tif"
diff --git a/virtualizarr/xarray.py b/virtualizarr/xarray.py
index bcd63b20..e868589e 100644
--- a/virtualizarr/xarray.py
+++ b/virtualizarr/xarray.py
@@ -21,7 +21,7 @@
 from xarray.core.types import NestedSequence
 from xarray.structure.combine import _infer_concat_order_from_positions, _nested_combine
 
-from virtualizarr.manifests import ManifestStore
+from virtualizarr.manifests import ManifestArray, ManifestGroup, ManifestStore
 from virtualizarr.manifests.manifest import validate_and_normalize_path_to_uri
 from virtualizarr.parallel import get_executor
 from virtualizarr.parsers.typing import Parser
@@ -35,6 +35,68 @@
     )
 
 
+def open_virtual_datatree(
+    url: str,
+    registry: ObjectStoreRegistry,
+    parser: Parser,
+    *,
+    drop_variables: Iterable[str] | None = None,
+    loadable_variables: Iterable[str] | None = None,
+    decode_times: bool | None = None,
+) -> xr.DataTree:
+    """
+    Open an archival data source as an [xarray.Datatree][] wrapping virtualized zarr arrays.
+
+    No data variables will be loaded unless specified in the ``loadable_variables`` kwarg (in which case they will open as lazily indexed arrays using xarray's standard lazy indexing classes).
+
+    Xarray indexes can optionally be created (the default behaviour is to create indexes for any 1D coordinate variables). To avoid creating any xarray indexes pass ``indexes={}``.
+
+    Parameters
+    ----------
+    url
+        The url of the data source to virtualize. The URL should include a scheme. For example:
+
+        - `url="file:///Users/my-name/Documents/my-project/my-data.nc"` for a local data source.
+        - `url="s3://my-bucket/my-project/my-data.nc"` for a remote data source on an S3 compatible cloud.
+
+    registry
+        An [ObjectStoreRegistry][virtualizarr.registry.ObjectStoreRegistry] for resolving urls and reading data.
+    parser
+        A parser to use for the given data source. For example:
+
+        - [virtualizarr.parsers.HDFParser][] for virtualizing NetCDF4 or HDF5 files.
+        - [virtualizarr.parsers.FITSParser][] for virtualizing FITS files.
+        - [virtualizarr.parsers.NetCDF3Parser][] for virtualizing NetCDF3 files.
+        - [virtualizarr.parsers.KerchunkJSONParser][] for re-opening Kerchunk JSONs.
+        - [virtualizarr.parsers.KerchunkParquetParser][] for re-opening Kerchunk Parquets.
+        - [virtualizarr.parsers.ZarrParser][] for virtualizing Zarr stores.
+        - [virtualizarr.parsers.ZarrParser][] for virtualizing Zarr stores.
+    drop_variables
+        Variables in the data source to drop before returning.
+    loadable_variables
+        Variables in the data source to load as Dask/NumPy arrays instead of as virtual arrays.
+    decode_times
+        Bool that is passed into [xarray.open_dataset][]. Allows time to be decoded into a datetime object.
+
+    Returns
+    -------
+    vds
+        An [xarray.DataTree][] containing virtual chunk references for all variables.
+    """
+    filepath = validate_and_normalize_path_to_uri(url, fs_root=Path.cwd().as_uri())
+
+    manifest_store = parser(
+        url=filepath,
+        registry=registry,
+    )
+
+    return manifest_store.to_virtual_datatree(
+        loadable_variables=loadable_variables,
+        decode_times=decode_times,
+        drop_variables=drop_variables,
+    )
+
+
 def open_virtual_dataset(
     url: str,
     registry: ObjectStoreRegistry,
@@ -354,6 +416,44 @@ def construct_virtual_dataset(
         )
 
 
+def construct_virtual_datatree(
+    manifest_store: ManifestStore,
+    group: str = "",
+    *,
+    drop_variables: Iterable[str] | None = None,
+    loadable_variables: Iterable[str] | None = None,
+    decode_times: bool | None = None,
+) -> xr.DataTree:
+    """
+    Construct a fully or partly virtual datatree from a ManifestStore.
+    """
+    fully_loadable_datatree = xr.open_datatree(
+        manifest_store,  # type: ignore[arg-type]
+        group=group,
+        engine="zarr",
+        consolidated=False,
+        zarr_format=3,
+        decode_times=decode_times,
+    )
+    if group:
+        node = manifest_store._group[group]
+    else:
+        node = manifest_store._group
+    if isinstance(node, ManifestArray):
+        node = ManifestGroup(arrays={group: node}, attributes={})
+    fully_virtual_datatree = node.to_virtual_datatree()
+
+    partially_loaded_datasets = {}
+    for name, virtual_node in fully_virtual_datatree.subtree_with_keys:
+        loadable_node = fully_loadable_datatree[name]
+        node_dataset = replace_virtual_with_loadable_vars(
+            virtual_node.to_dataset(), loadable_node.to_dataset(), loadable_variables
+        )
+        node_dataset = node_dataset.drop_vars(list(drop_variables or ()))
+        partially_loaded_datasets[name] = node_dataset
+    return xr.DataTree.from_dict(partially_loaded_datasets)
+
+
 def replace_virtual_with_loadable_vars(
     fully_virtual_ds: xr.Dataset,
     loadable_ds: xr.Dataset,

From 5c35e1b3f922a0255ea943723d1d06f97a238281 Mon Sep 17 00:00:00 2001
From: Max Jones <14077947+maxrjones@users.noreply.github.com>
Date: Fri, 14 Nov 2025 12:36:04 -0500
Subject: [PATCH 5/7] Remove unused function

---
 virtualizarr/manifests/group.py | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/virtualizarr/manifests/group.py b/virtualizarr/manifests/group.py
index 3a5a6091..e51a0141 100644
--- a/virtualizarr/manifests/group.py
+++ b/virtualizarr/manifests/group.py
@@ -75,11 +75,6 @@ def groups(self) -> dict[str, "ManifestGroup"]:
         """Subgroups contained in this group."""
         return {k: v for k, v in self._members.items() if isinstance(v, ManifestGroup)}
 
-    @property
-    def contains_groups(self) -> bool:
-        """True if this group has subgroups."""
-        return any(isinstance(v, ManifestGroup) for v in self._members.values())
-
     def __getitem__(self, path: str) -> "ManifestArray | ManifestGroup":
         """Obtain a group member."""
         if "/" in path:

From e563aa0d2e70a06e1ea038492f215a5ed32cb35b Mon Sep 17 00:00:00 2001
From: Max Jones <14077947+maxrjones@users.noreply.github.com>
Date: Fri, 14 Nov 2025 12:50:43 -0500
Subject: [PATCH 6/7] Fix cross-reference

---
 virtualizarr/manifests/store.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/virtualizarr/manifests/store.py b/virtualizarr/manifests/store.py
index d72b70e7..a5dff589 100644
--- a/virtualizarr/manifests/store.py
+++ b/virtualizarr/manifests/store.py
@@ -383,7 +383,7 @@ def to_virtual_datatree(
         decode_times: bool | None = None,
     ) -> "xr.DataTree":
         """
-        Create a "virtual" [xarray.Datatree][] containing the contents of a zarr group. Default is the root group and all sub-groups.
+        Create a "virtual" [xarray.DataTree][] containing the contents of a zarr group. Default is the root group and all sub-groups.
 
         Will ignore the contents of any other groups in the store.
 
@@ -401,7 +401,7 @@ def to_virtual_datatree(
 
         Returns
         -------
-        vdt : xarray.Datatree
+        vdt : xarray.DataTree
         """
 
         from virtualizarr.xarray import construct_virtual_datatree

From 0f45437033808482a88ab09b23127280b651ce6b Mon Sep 17 00:00:00 2001
From: Max Jones <14077947+maxrjones@users.noreply.github.com>
Date: Fri, 14 Nov 2025 12:54:12 -0500
Subject: [PATCH 7/7] Fixup docstrings

---
 virtualizarr/manifests/group.py | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/virtualizarr/manifests/group.py b/virtualizarr/manifests/group.py
index e51a0141..d226e844 100644
--- a/virtualizarr/manifests/group.py
+++ b/virtualizarr/manifests/group.py
@@ -128,9 +128,11 @@ def to_virtual_dataset(self) -> xr.Dataset:
 
     def to_virtual_datasets(self) -> dict[str, xr.Dataset]:
         """
-        Create a "virtual" [xarray.DataTree][] containing the contents of one zarr group.
+        Create a dictionary containing virtual datasets for all the sub-groups of a ManifestGroup. All the
+        variables in the datasets will be "virtual", i.e., they will wrap ManifestArray objects.
 
-        All variables in the returned DataTree will be "virtual", i.e. they will wrap ManifestArray objects.
+        It is convenient to have a separate `to_virtual_datasets` function from `to_virtual_datatree` so that
+        it can be called recursively without needing to use `DataTree.to_dict() and `.from_dict()` repeatedly.
         """
         result = {"": self.to_virtual_dataset()}
 
@@ -150,5 +152,10 @@ def to_virtual_datasets(self) -> dict[str, xr.Dataset]:
         return result
 
     def to_virtual_datatree(self) -> xr.DataTree:
+        """
+        Create a "virtual" [xarray.DataTree][] containing the contents of one zarr group.
+
+        All variables in the returned DataTree will be "virtual", i.e. they will wrap ManifestArray objects.
+        """
         datasets = self.to_virtual_datasets()
         return xr.DataTree.from_dict(datasets)