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Allow zarr 3.3; strictly exclude root node from consolidated metadata #31

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Merged
eagmon merged 2 commits into from
Aug 21, 2026
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Allow zarr 3.3; strictly exclude root node from consolidated metadata #31

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bfedbbd
chore(deps): allow zarr 3.3 (widen xarray-extra pin to >=3.1.6,<3.4)
eagmon Aug 21, 2026
63fd78c
fix(xarray): strictly exclude root node from consolidated metadata
eagmon Aug 21, 2026
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4 changes: 2 additions & 2 deletions pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@ parquet = [
]
xarray = [
"xarray>=2026.04",
"zarr~=3.1.6",
"zarr>=3.1.6,<3.4",
"zarrs>=0.2",
"pint",
"unum",
Expand All @@ -41,7 +41,7 @@ dev = [
"fsspec",
"tqdm",
"xarray>=2026.04",
"zarr~=3.1.6",
"zarr>=3.1.6,<3.4",
"zarrs>=0.2",
"pint",
"unum",
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6 changes: 3 additions & 3 deletions uv.lock
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14 changes: 10 additions & 4 deletions viva_emitters/xarray_emitter/zarr_writer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -156,8 +156,11 @@ async def consolidate_metadata(
k: v.metadata
async for (k, v) in
group.members(max_depth=None, use_consolidated_for_children=False)}
# TODO: fix in `consolidate_metadata()` (zarr==3.1.6)
members_metadata |= {"": group.metadata}
# The root node is STRICTLY EXCLUDED from consolidated metadata: a "" entry
# is a self-reference that risks infinite loops in Zarr traversal functions
# (e.g. Group.tree()), not only ConsolidatedMetadata._flat_to_nested(). The
# root's own metadata lives on `group` itself. (Per @ntfrgl on PR #31;
# mirrors vEcoli be603b5d.)

# combine and write consolidated metadata
for k, v in members_metadata.items():
Expand Down Expand Up @@ -208,11 +211,14 @@ async def reconsolidate_metadata(
# read metadata at updated paths
group = _replace_consolidated_metadata(group, None)
mod_members_metadata, add_members_metadata = [
{k: n.metadata async for (k, n) in _iter_from_keys(group, keys)}
# `if k` strictly excludes the root node: a "" entry is a self-reference
# that risks infinite loops in Zarr traversal functions (see
# consolidate_metadata above).
{k: n.metadata async for (k, n) in _iter_from_keys(group, keys) if k}
for keys in [modified_keys, added_keys]]

# check assumptions about metadata updates
old_keys = set(members_metadata.keys()) | {""}
old_keys = set(members_metadata.keys())
assert set(mod_members_metadata.keys()).issubset(old_keys)
assert set(add_members_metadata.keys()).isdisjoint(old_keys)

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