Track upstream neuroconv zarr 3 support; drop the zarr<3 pin when it ships #129

🤖 AI text below 🤖

Duplicate record of tabedzki/tank-lab-to-nwb#2 — kept in both repos; update both when status changes.

Summary

A fresh install of neuroconv currently fails at import, which breaks the NWB export's converter (tank-lab-to-nwb). We pin zarr<3 as a stopgap. This issue tracks upstream neuroconv's zarr 3 support so we know when to drop the pin.

Cause

• neuroconv (through the latest release, 0.10.2) uses the zarr 2 API at import time: zarr.codec_registry in neuroconv/tools/nwb_helpers/_configuration_models/_zarr_dataset_io.py:15.
• neuroconv does not bound zarr itself; it only requires hdmf_zarr>=0.11.
• hdmf-zarr 0.14.0 migrated to zarr 3 (Migrate hdmf-zarr from zarr-python v2 to v3 hdmf-dev/hdmf-zarr#325) and requires zarr>=3.4. The resolver now picks hdmf-zarr 0.14 + zarr 3.4, and the import fails:

AttributeError: module 'zarr' has no attribute 'codec_registry'

Verified 2026-09-25 in a clean Python 3.12 venv:

• neuroconv[scanimage,suite2p] alone → zarr 3.4.0 / hdmf-zarr 0.14.0 → import fails.
• Adding zarr<3 → zarr 2.18.7 / hdmf-zarr 0.13.0 / numcodecs 0.15.1 → import works. No hdmf-zarr cap needed.

Our stopgap

zarr<3 added to tank-lab-to-nwb dependencies, with a regression test (tests/test_dependency_pins.py) that fails under zarr 3 and passes under zarr 2:
branch tabedzki/build/pin-zarr-lt3 (off building-nwb-converter), commit tabedzki/tank-lab-to-nwb@877892e.

uv.lock was not regenerated because [tool.uv.sources] points at sibling paths that don't resolve. The locked zarr (2.18.4) already satisfies the pin.

Upstream items to track

When to act

• neuroconv release containing #2063 (≥ 0.10.3): our pin becomes redundant but harmless; keep it until the next item.
• neuroconv release containing #1749 (zarr 3 support): remove zarr<3 from tank-lab-to-nwb, update tests/test_dependency_pins.py (drop the < 3 assertion, keep the import check), relock.

We write HDF5 NWB files, so zarr only matters because neuroconv imports it. We don't need zarr 3 features.