[guijacquemet]

Summary

Fixes #38.

• masks.py: when an OME-Zarr image's labels group cannot be read, _label_masks now returns its path, <image>/labels. Examples are a group that does not list its label images, or a store that fails to open. find_masks reports these paths under the existing error unreadable_mask, together with masks whose headers cannot be opened.
• Without the zarr extra, label images are still skipped quietly, as find_masks documents. In that case the OME-Zarr image itself is unreadable and already reported.
• Docs: contract §15 (header checks) and the unreadable_mask row in user guide §8 now cover this case.

Why

The NgffError was logged at info level and then ignored. If every image of a mask type was affected, that type disappeared from the inventory and mask_missing never fired. Those objects were then not measured, and nothing said so.

Notes for review

• No new error code: the existing unreadable_mask is reused, with an extended action text.
• The manifest and outputs do not change for valid stores.

Tests

• New regression test: tests/test_masks.py::test_a_malformed_labels_group_is_an_error_not_a_vanished_mask_type. It uses two OME-Zarr images whose labels attribute is not a list. It checks both preflight and that run_experiment is blocked.
• Fails on main: the inventory is MaskInventory(types=(), files=(), issues=()) and .ok is True.
• Full suite (Python 3.13, zarr 3.4.2, notebook extra installed): 1052 passed, 1 skipped. The skip is test_discovery.py:472: running as root ignores file modes.
• ruff check . and ruff format --check . are clean.
• Not run: zarr 2.18 / Python 3.11, Windows, macOS.

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Generated by Claude Code

[guijacquemet]

Merged main (#40, #42, #43, #44) in:

• _header_issues keeps Give masks a plane identity (Z/T); refuse 2D masks of multi-plane images #43's Z/T plane checks and takes Report a malformed OME-Zarr labels group as unreadable_mask #41's unreadable labels groups;
• contract §15 header checks combine Z/T axes, the uint64 note and the <image>/labels unreadable_mask rule;
• the user guide keeps Give masks a plane identity (Z/T); refuse 2D masks of multi-plane images #43's mask_not_2d text and Report a malformed OME-Zarr labels group as unreadable_mask #41's unreadable_mask text;
• all tests were kept.

1121 passed, 1 skipped (test_discovery.py:472, root), ruff clean, CI 7/7 green on 0ddd360. Merging.

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Generated by Claude Code