[guijacquemet]

Summary

Two MorphoBricks alignment changes, one commit each. The branch name is fixed for this work, so both are in this PR instead of the usual one PR per change.

Commit 1: fill position_id (D02, audit finding X02)

plane_histograms.csv had a position_id column that this brick never filled, and the run manifest had no position identity per file.

• discovery:
  • New public position_id(image). It returns the image name without .tif/.tiff/.zarr (any case) and without a preceding .ome, so img_01.ome.tif gives img_01. It is re-exported from the package.
  • New error duplicate_position_id: two images in one leaf folder that share an identifier, ignoring case, are refused.
• run: every CSV row now carries position_id, including rows from converted TIFFs. Rows reused from an earlier table with blank position_id are filled from the path without reading pixels.
• manifest: new optional per-file key position_id (FileEntry.position_id). Manifests written before this change read it as null.
• Docs: contract §1, §5, §8 and §9; plan §6, §10 and §12 question 20; user guide §2, §6 and §8; AGENTS.md.

Commit 2: require Python 3.11 (D01)

• requires-python >=3.11 and Ruff target py311. Ruff then asks for two upgrades:
  • datetime.UTC
  • Severity as a StrEnum. It is only read through .value, so text output is unchanged.
• Notebook Step 0 and its test refuse Python 3.10.
• The CI matrix is now 3.11 and 3.13. The 3.11 jobs pin zarr>=2.18,<3, because zarr 3 also supports 3.11 and the zarr 2 path would otherwise go untested. Before, the 3.10 jobs covered zarr 2.
• AGENTS, the development guide and the user guide now say 3.11.

Decisions implemented

These are the MorphoBricks owner decisions of 2026-10-26 (CellMigrationLab/MorphoFeature#6, decision ledger):

• D02: the canonical FOV key is condition + biological_repeat + technical_repeat + position_id. position_id falls back to the file stem only when one file is exactly one position. That always holds here, because several series and position-like axes are already errors.
• D01: every brick requires Python ≥3.11.

Versioning: the CSV columns and schema_version 2 are unchanged. The manifest stays at version 1 with one optional key.

Notes for review

• The normalization contract §8.2 said position_id is "never inferred from file names". That conflicts with D02 and is corrected in Require Python 3.11; position_id follows the MorphoBricks FOV key morphobricks-normalization#4, together with Python 3.11 there.
• Excluding one of two duplicate images does not clear duplicate_position_id; the message says to rename or move one.
• a.tif and a.ome.tif in one folder used to both convert to a.ome.zarr. That pair is now refused.
• Not verified: CI on Windows and macOS. All results below are local runs on Linux.

Tests (local)

Python	zarr	ruff check	ruff format --check	pytest
3.11.17	2.18.7	All checks passed	53 files already formatted	754 passed, 14 skipped
3.13.17	3.4.1			767 passed, 1 skipped

• On 3.11 the skips are the OME-NGFF 0.5 tests that need zarr 3, plus the POSIX-permission test. On 3.13 only the permission test skips; the sandbox ignores file modes.
• Without commit 1's source change, 8 of its new tests fail.

Do not merge without the owner's go-ahead.

🤖 Generated with Claude Code

https://claude.ai/code/session_01U6vJfhGWQ7pTpsJhw48Zf7