Allow zarr 3.3; strictly exclude root node from consolidated metadata

[eagmon]

vEcoli PR #414 moved onto zarr 3.3. This makes viva-emitters compatible so downstreams (v2ecoli, the map-reduce engine #32) can adopt it.

Changes

1. Widen the [xarray]/[dev] pin zarr~=3.1.6 → zarr>=3.1.6,<3.4. The full suite passes unchanged on both zarr 3.1.6 (the locked default) and zarr 3.3.0 (fresh venv). Universal resolution keeps the lock on 3.1.6 (Python-3.11-compatible); the widened range lets a Python-3.12 downstream select 3.3. Bounded at <3.4 because the emitter uses zarr-internal symbols.
2. Strictly exclude the root node from consolidated metadata (consolidate_metadata / reconsolidate_metadata). Per @ntfrgl's review: a "" root entry is a self-reference that risks infinite loops in Zarr traversal functions beyond _flat_to_nested() (e.g. Group.tree()). viva already carries a custom group_tree_async() with an explicit if key == "": continue self-loop guard precisely to survive that root entry — which confirms the hazard. The root's own metadata still lives on the group itself, so readers keep seeing root attrs (provenance test passes). Mirrors vEcoli be603b5d.

Correction to my earlier note: I first concluded no consolidation change was needed because zarr 3.3.0's _flat_to_nested() still tolerates the root key. That basis was too narrow — the exclusion is about latent infinite-loop risk in other traversal functions, not just _flat_to_nested. Fixed.

Python support

zarr 3.3 dropped Python 3.11, but the [xarray] backend is already 3.12-only at runtime (ImportError guard). requires-python stays >=3.11 for the SQLite/parquet emitters.

Follow-up

With the root excluded, the self-loop guard in the (currently unused) group_tree_async() is now moot and could be removed in a separate cleanup.

Verification

Full suite passes on zarr 3.1.6 (107) and zarr 3.3.0 (107), incl. consolidate/reconsolidate/append/provenance/colony.

Part of the PR #414 reconciliation (follows #29, #30; precedes #32).

🤖 Generated with Claude Code

[ntfrgl]

Root node metadata should be strictly excluded from Zarr's consolidated metadata, in order to avoid potential infinite loops in Zarr library functions besides ConsolidatedMetadata._flat_to_nested(). For example, this was the purpose of the custom version of Group.tree() with an explicit guard, which could be removed in CovertLab/vEcoli@be603b5.

[eagmon]

Fixed in 63fd78c — the root node is now strictly excluded from consolidated metadata in both consolidate_metadata() and reconsolidate_metadata().

You're right that my original basis was too narrow: I'd checked only that zarr 3.3.0's ConsolidatedMetadata._flat_to_nested() still tolerates the "" key, and missed the broader traversal-function hazard. viva's own custom group_tree_async() with the if key == "": continue self-loop guard is exactly the evidence — it exists to survive the root entry. With the root now excluded, that guard is moot; I've left removing it (and the unused custom group_tree, in favor of Group.tree()) as a follow-up cleanup rather than expand this PR.

Verified the full suite on both zarr 3.1.6 and 3.3.0 (107 each), including consolidate/reconsolidate/append/provenance/colony; root attrs (provenance) still read back fine since the root's metadata lives on the group itself.